Biological markers predictive of anti-cancer response to epidermal growth factor receptor kinase inhibitors

ABSTRACT

The present invention provides diagnostic and prognostic methods for predicting the effectiveness of treatment of a cancer patient with an EGFR kinase inhibitor. Methods are provided for predicting the sensitivity of tumor cell growth to inhibition by an EGFR kinase inhibitor, comprising assessing whether the tumor cell has undergone an epithelial to mesenchymal transition (EMT), by determining the expression level of epithelial and/or mesenchymal biomarkers, wherein tumor cells that have undergone an EMT are substantially less sensitive to inhibition by EGFR kinase inhibitors. Improved methods for treating cancer patients with EGFR kinase inhibitors that incorporate the above methodology are also provided. Additionally, methods are provided for the identification of new biomarkers that are predictive of responsiveness of tumors to EGFR kinase inhibitors. Furthermore, methods for the identification of agents that restore the sensitivity of tumor cells that have undergone EMT to inhibition by EGFR kinase inhibitors are also provided.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application claims the benefit of U.S. Provisional Application No.60/662,545, filed Mar. 16, 2005, and U.S. Provisional Application No.60/671,821, filed Apr. 15, 2005, both of which are herein incorporatedby reference in their entirety.

BACKGROUND OF THE INVENTION

The present invention is directed to methods for diagnosing and treatingcancer patients. In particular, the present invention is directed tomethods for determining which patients will most benefit from treatmentwith an epidermal growth factor receptor (EGFR) kinase inhibitor.

Cancer is a generic name for a wide range of cellular malignanciescharacterized by unregulated growth, lack of differentiation, and theability to invade local tissues and metastasize. These neoplasticmalignancies affect, with various degrees of prevalence, every tissueand organ in the body.

A multitude of therapeutic agents have been developed over the past fewdecades for the treatment of various types of cancer. The most commonlyused types of anticancer agents include: DNA-alkylating agents (e.g.,cyclophosphamide, ifosfamide), antimetabolites (e.g., methotrexate, afolate antagonist, and 5-fluorouracil, a pyrimidine antagonist),microtubule disrupters (e.g., vincristine, vinblastine, paclitaxel), DNAintercalators (e.g., doxorubicin, daunomycin, cisplatin), and hormonetherapy (e.g., tamoxifen, flutamide).

The epidermal growth factor receptor (EGFR) family comprises fourclosely related receptors (HER1/EGFR, HER2, HER3 and HER4) involved incellular responses such as differentiation and proliferation.Over-expression of the EGFR kinase, or its ligand TGF-alpha, isfrequently associated with many cancers, including breast, lung,colorectal, ovarian, renal cell, bladder, head and neck cancers,glioblastomas, and astrocytomas, and is believed to contribute to themalignant growth of these tumors. A specific deletion-mutation in theEGFR gene (EGFRvIII) has also been found to increase cellulartumorigenicity. Activation of EGFR stimulated signaling pathways promotemultiple processes that are potentially cancer-promoting, e.g.proliferation, angiogenesis, cell motility and invasion, decreasedapoptosis and induction of drug resistance. Increased HER1/EGFRexpression is frequently linked to advanced disease, metastases and poorprognosis. For example, in NSCLC and gastric cancer, increased HER1/EGFRexpression has been shown to correlate with a high metastatic rate, poortumor differentiation and increased tumor proliferation.

Mutations which activate the receptor's intrinsic protein tyrosinekinase activity and/or increase downstream signaling have been observedin NSCLC and glioblastoma. However the role of mutations as a principlemechanism in conferring sensitivity to EGF receptor inhibitors, forexample erlotinib (TARCEVA™) or gefitinib (IRESSA™), has beencontroversial. Recently, a mutant form of the full length EGF receptorhas been reported to predict responsiveness to the EGF receptor tyrosinekinase inhibitor gefitinib (Paez, J. G. et al. (2004) Science304:1497-1500; Lynch, T. J. et al. (2004) N. Engl. J. Med.350:2129-2139). Cell culture studies have shown that cell lines whichexpress the mutant form of the EGF receptor (i.e. H3255) were moresensitive to growth inhibition by the EGF receptor tyrosine kinaseinhibitor gefitinib, and that much higher concentrations of gefitinibwas required to inhibit the tumor cell lines expressing wild type EGFreceptor. These observations suggests that specific mutant forms of theEGF receptor may reflect a greater sensitivity to EGF receptorinhibitors, but do not identify a completely non-responsive phenotype.

The development for use as anti-tumor agents of compounds that directlyinhibit the kinase activity of the EGFR, as well as antibodies thatreduce EGFR kinase activity by blocking EGFR activation, are areas ofintense research effort (de Bono J. S. and Rowinsky, E. K. (2002) Trendsin Mol. Medicine 8:S19-S26; Dancey, J. and Sausville, E. A. (2003)Nature Rev. Drug Discovery 2:92-313). Several studies have demonstrated,disclosed, or suggested that some EGFR kinase inhibitors might improvetumor cell or neoplasia killing when used in combination with certainother anti-cancer or chemotherapeutic agents or treatments (e.g. Herbst,R. S. et al. (2001) Expert Opin. Biol. Ther. 1:719-732; Solomon, B. etal (2003) Int. J. Radiat. Oncol. Biol. Phys. 55:713-723; Krishnan, S. etal. (2003) Frontiers in Bioscience 8, el-13; Grunwald, V. and Hidalgo,M. (2003) J. Nat. Cancer Inst. 95:851-867; Seymour L. (2003) CurrentOpin. Investig. Drugs 4(6):658-666; Khalil, M. Y. et al. (2003) ExpertRev. Anticancer Ther.3:367-380; Bulgaru, A. M. et al. (2003) Expert Rev.Anticancer Ther.3:269-279; Dancey, J. and Sausville, E. A. (2003) NatureRev. Drug Discovery 2:92-313; Ciardiello, F. et al. (2000) Clin. CancerRes. 6:2053-2063; and Patent Publication No: US 2003/0157104).

Erlotinib (e.g. erlotinib HCl, also known as TARCEVA™ or OSI-774) is anorally available inhibitor of EGFR kinase. In vitro, erlotinib hasdemonstrated substantial inhibitory activity against EGFR kinase in anumber of human tumor cell lines, including colorectal and breast cancer(Moyer J. D. et al. (1997) Cancer Res. 57:4838), and preclinicalevaluation has demonstrated activity against a number of EGFR-expressinghuman tumor xenografts (Pollack, V. A. et al (1999) J. Pharmacol. Exp.Ther. 291:739). More recently, erlotinib has demonstrated promisingactivity in phase I and II trials in a number of indications, includinghead and neck cancer (Soulieres, D., et al. (2004) J. Clin. Oncol.22:77), NSCLC (Perez-Soler R, et al. (2001) Proc. Am. Soc. Clin. Oncol.20:310a, abstract 1235), CRC (Oza, M., et al. (2003) Proc. Am. Soc.Clin. Oncol. 22:196a, abstract 785) and MBC (Winer, E., et al. (2002)Breast Cancer Res. Treat. 76:5115a, abstract 445). In a phase III trial,erlotinib monotherapy significantly prolonged survival, delayed diseaseprogression and delayed worsening of lung cancer-related symptoms inpatients with advanced, treatment-refractory NSCLC (Shepherd, F. et al.(2004) J. Clin. Oncology, 22:14S (July 15 Supplement), Abstract 7022).While most of the clinical trial data for erlotinib relate to its use inNSCLC, preliminary results from phase I/II studies have demonstratedpromising activity for erlotinib and capecitabine/erlotinib combinationtherapy in patients with wide range of human solid tumor types,including CRC (Oza, M., et al. (2003) Proc. Am. Soc. Clin. Oncol.22:196a, abstract 785) and MBC (Jones, R. J., et al. (2003) Proc. Am.Soc. Clin. Oncol. 22:45a, abstract 180). In November 2004 the U.S. Foodand Drug Administration (FDA) approved TARCEVA™ for the treatment ofpatients with locally advanced or metastatic non-small cell lung cancer(NSCLC) after failure of at least one prior chemotherapy regimen.TARCEVA™ is the only drug in the epidermal growth factor receptor (EGFR)class to demonstrate in a Phase III clinical trial an increase insurvival in advanced NSCLC patients.

An anti-neoplastic drug would ideally kill cancer cells selectively,with a wide therapeutic index relative to its toxicity towardsnon-malignant cells. It would also retain its efficacy against malignantcells, even after prolonged exposure to the drug. Unfortunately, none ofthe current chemotherapies possess such an ideal profile. Instead, mostpossess very narrow therapeutic indexes. Furthermore, cancerous cellsexposed to slightly sub-lethal concentrations of a chemotherapeuticagent will very often develop resistance to such an agent, and quiteoften cross-resistance to several other antineoplastic agents as well.Additionally, for any given cancer type one frequently cannot predictwhich patient is likely to respond to a particular treatment, even withnewer gene-targeted therapies, such as EGFR kinase inhibitors, thusnecessitating considerable trial and error, often at considerable riskand discomfort to the patient, in order to find the most effectivetherapy.

Thus, there is a need for more efficacious treatment for neoplasia andother proliferative disorders, and for more effective means fordetermining which tumors will respond to which treatment. Strategies forenhancing the therapeutic efficacy of existing drugs have involvedchanges in the schedule for their administration, and also their use incombination with other anticancer or biochemical modulating agents.Combination therapy is well known as a method that can result in greaterefficacy and diminished side effects relative to the use of thetherapeutically relevant dose of each agent alone. In some cases, theefficacy of the drug combination is additive (the efficacy of thecombination is approximately equal to the sum of the effects of eachdrug alone), but in other cases the effect is synergistic (the efficacyof the combination is greater than the sum of the effects of each druggiven alone).

Target-specific therapeutic approaches, such as erlotinib, are generallyassociated with reduced toxicity compared with conventional cytotoxicagents, and therefore lend themselves to use in combination regimens.Promising results have been observed in phase I/II studies of erlotinibin combination with bevacizumab (Mininberg, E. D., et al. (2003) Proc.Am. Soc. Clin. Oncol. 22:627a, abstract 2521) and gemcitabine(Dragovich, T., (2003) Proc. Am. Soc. Clin. Oncol. 22:223a, abstract895). Recent data in NSCLC phase III trials have shown that first-lineerlotinib or gefitinib in combination with standard chemotherapy did notimprove survival (Gatzemeier, U., (2004) Proc. Am. Soc. Clin. Oncol.23:617 (Abstract 7010); Herbst, R. S., (2004) Proc. Am. Soc. Clin.Oncol. 23:617 (Abstract 7011); Giaccone, G., et al. (2004) J. Clin.Oncol. 22:777; Herbst, R., et al. (2004) J. Clin. Oncol. 22:785).However, pancreatic cancer phase III trials have shown that first-lineerlotinib in combination with gemcitabine did improve survival (OSIPharmaceuticals/Genentech/Roche Pharmaceuticals Press Release, 9/20/04).

Several groups have investigated potential biomarkers to predict apatient's response to EGFR inhibitors (see for example, PCTpublications: WO 2004/063709, WO 2005/017493, WO 2004/111273, WO2004/071572, WO 2005/117553 and WO 2005/070020; and US published patentapplications: US 2005/0019785, and US 2004/0132097). However, nodiagnostic or prognostic tests have yet emerged that can guidepracticing physicians in the treatment of their patients with EGFRkinase inhibitors.

During most cancer metastases, an important change occurs in a tumorcell known as the epithelial-mesenchymal transition (EMT) (Thiery, J. P.(2002) Nat. Rev. Cancer 2:442-454; Savagner, P. (2001) Bioessays23:912-923; Kang Y. and Massague, J. (2004) Cell 118:277-279;Julien-Grille, S., et al. Cancer Research 63:2172-2178; Bates, R. C. etal. (2003) Current Biology 13:1721-1727; Lu Z., et al. (2003) CancerCell. 4(6):499-515)). Epithelial cells, which are bound together tightlyand exhibit polarity, give rise to mesenchymal cells, which are heldtogether more loosely, exhibit a loss of polarity, and have the abilityto travel. These mesenchymal cells can spread into tissues surroundingthe original tumor, as well as separate from the tumor, invade blood andlymph vessels, and travel to new locations where they divide and formadditional tumors. EMT does not occur in healthy cells except duringembryogenesis. Under normal circumstances TGF-β acts as a growthinhibitor. However it is believed that during cancer metastasis, TGF-βbegins to promote EMT.

Thus, there remains a critical need for improved methods for determiningthe best mode of treatment for any given cancer patient and for theincorporation of such determinations into more effective treatmentregimens for cancer patients, whether such inhibitors are used as singleagents or combined with other anti-cancer agents.

SUMMARY OF THE INVENTION

The present invention provides diagnostic and prognostic methods forpredicting the effectiveness of treatment of a cancer patient with anEGFR kinase inhibitor. Based on the surprising discovery that thesensitivity of tumor cell growth to inhibition by EGFR kinase inhibitorsis dependent on whether such tumor cells have undergone an EMT, methodshave been devised for determining epithelial and/or mesenchymalbiomarkers to predict the sensitivity of tumor cells to EGFR kinaseinhibitors.

Accordingly, the present invention provides a method of predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, comprising: assessing the level of an epithelial biomarkerexpressed by a tumor cell; and predicting the sensitivity of tumor cellgrowth to inhibition by an EGFR kinase inhibitor, wherein highexpression levels of tumor cell epithelial biomarkers correlate withhigh sensitivity to inhibition by EGFR kinase inhibitors.

The present invention also provides a method of predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, comprising: assessing the level of a mesenchymal biomarkerexpressed by a tumor cell; and predicting the sensitivity of tumor cellgrowth to inhibition by an EGFR kinase inhibitor, wherein highexpression levels of tumor cell mesenchymal biomarkers correlate withlow sensitivity to inhibition by EGFR kinase inhibitors.

Improved methods for treating cancer patients with EGFR kinaseinhibitors that incorporate the above methodology are also provided.Thus, the present invention further provides a method for treatingtumors or tumor metastases in a patient, comprising the steps ofdiagnosing a patient's likely responsiveness to an EGFR kinase inhibitorby assessing whether the tumor cells have undergone anepithelial-mesenchymal transition, and administering to said patient atherapeutically effective amount of an EGFR kinase inhibitor.

Additionally, methods are provided for the identification of newepithelial or mesenchymal biomarkers that are predictive ofresponsiveness of tumors to EGFR kinase inhibitors.

Thus, for example, the present invention further provides a method ofidentifying an epithelial biomarker that is diagnostic for moreeffective treatment of a neoplastic condition with an EGFR kinaseinhibitor, comprising: measuring the level of a candidate epithelialbiomarker in neoplastic cell-containing samples from patients with aneoplastic condition, and identifying a correlation between the level ofsaid candidate epithelial biomarker in the sample from the patient withthe effectiveness of treatment of the neoplastic condition with an EGFRkinase inhibitor, wherein a correlation of high levels of the epithelialbiomarker with more effective treatment of the neoplastic condition withan EGFR kinase inhibitor indicates that said epithelial biomarker isdiagnostic for more effective treatment of the neoplastic condition withan EGFR kinase inhibitor.

The present invention further provides a method of identifying amesenchymal biomarker that is diagnostic for less effective treatment ofa neoplastic condition with an EGFR kinase inhibitor, comprising: (a)measuring the level of a candidate mesenchymal biomarker in neoplasticcell-containing samples from patients with a neoplastic condition, and(b) identifying a correlation between the level of said candidatemesenchymal biomarker in the sample from the patient with theeffectiveness of treatment of the neoplastic condition with an EGFRkinase inhibitor, wherein a correlation of high levels of themesenchymal biomarker with less effective treatment of the neoplasticcondition with an EGFR kinase inhibitor indicates that said mesenchymalbiomarker is diagnostic for less effective treatment of the neoplasticcondition with an EGFR kinase inhibitor.

Furthermore, methods for the identification of agents that restore thesensitivity of tumor cells that have undergone EMT to inhibition by EGFRkinase inhibitors are also provided. Thus, for example, the presentinvention provides a method for the identification of an agent thatenhances sensitivity of the growth of a tumor cell to an EGFR kinaseinhibitor, said tumor cell having being characterized as one that haspreviously undergone an epithelial-mesenchymal transition, comprisingcontacting a sample of said tumor cells with an EGFR kinase inhibitor,contacting an identical sample of said tumor cells with an EGFR kinaseinhibitor in the presence of a test agent, comparing the EGFR kinaseinhibitor-mediated growth inhibition in the presence and absence of thetest agent, and determining whether the test agent is an agent thatenhances sensitivity of the growth of the tumor cell to an EGFR kinaseinhibitor.

BRIEF DESCRIPTION OF THE FIGURES

The file of this patent contains at least one drawing executed in color.Copies of this patent with color drawing(s) will be provided by thePatent and Trademark Office upon request and payment of the necessaryfee.

FIG. 1: In vivo activity of erlotinib against NSCLC xenografts.

FIG. 2: A. Proteomic profiling of NSCLC lines, sensitive or relativelyinsensitive to EGFR kinase inhibition in vitro, showed markedlyincreased LC-MS/MS detection of vimentin and fibronectin peptides incell lines relatively insensitive to erlotinib. B. NSCLC lines sensitiveto EGF receptor inhibition express elevated levels of E-cadherin, withtrends observed for γ- and α-catenins. E-cadherin immunoblots wereperformed with two distinct antibodies with similar results (data notshown). NSCLC lines relatively insensitive to growth inhibition byerlotinib expressed the mesenchymal proteins vimentin and/orfibronectin. No relationship between total EGF receptor proteinexpression and sensitivity was observed, though all lines testedexpressed detectable EGF receptor. C. Confocal microscopy of NSCLC linessensitive to growth inhibition by erlotinib, H292 and H441, showingmembrane expression of E-cadherin, but not in the cell lines Calu6 andH1703 that are relatively insensitive to erlotinib. Conversely, therelatively insensitive lines Calu6 and H1703 expressed intermediatefilament staining for vimentin, while the erlotinib sensitive lines H292and H441 did not.

FIG. 3: NSCLC lines were grown as subcutaneous xenografts in SCID miceto a volume of ˜500 mm³, excised and flash frozen in liquid nitrogen (4animals per cell line). Tumor tissue was pulverized while frozen,subjected to detergent lysis and SDS-PAGE as described and immunoblotsprobed with antibodies to E-cadherin, γ-catenin, Brk, fibronectin,vimentin, and GAPDH. Consistent with in vitro results, E-cadherinexpression was restricted to erlotinib sensitive lines and fibronectinto relatively insensitive lines.

FIG. 4: immunoblot showing higher Brk expression levels in NSCLC celllines that are most sensitive to EGFR kinase inhibition.

FIG. 5: A) Pancreatic cell lines sensitive to EGF receptor inhibitionexpress elevated levels of the epithelial cell junction proteinsE-cadherin and γ-catenin. The mesenchymal marker vimentin was mostabundant in the insensitive PANCl cells. B) Confocal microscopy of apancreatic cell line sensitive to growth inhibition by erlotinib, BxPC3,showing membrane expression of E-cadherin, but not in the cell lineMiaPaca2, that is relatively insensitive to erlotinib. Conversely, therelatively insensitive line MiaPaca2 expressed intermediate filamentstaining for vimentin, while the erlotinib sensitive line BxPC3 did not.

FIG. 6 a: Kaplan-Meier curve illustrating time to disease progression(TTP) is longer for patients receiving erlotinib in combination withchemotherapy compared to patients receiving chemotherapy only whosetumors with E-cadherin staining intensity of >=2. FIG. 6 b: Kaplan-Meiercurve illustrating time to disease progression (TTP) is not extended forpatients having tumor E-cadherin staining intensity of <=1 who aretreated with erlotinib in combination with chemotherapy compared topatients receiving chemotherapy alone.

DETAILED DESCRIPTION OF THE INVENTION

The term “cancer” in an animal refers to the presence of cellspossessing characteristics typical of cancer-causing cells, such asuncontrolled proliferation, immortality, metastatic potential, rapidgrowth and proliferation rate, and certain characteristic morphologicalfeatures. Often, cancer cells will be in the form of a tumor, but suchcells may exist alone within an animal, or may circulate in the bloodstream as independent cells, such as leukemic cells.

“Abnormal cell growth”, as used herein, unless otherwise indicated,refers to cell growth that is independent of normal regulatorymechanisms (e.g., loss of contact inhibition). This includes theabnormal growth of: (1) tumor cells (tumors) that proliferate byexpressing a mutated tyrosine kinase or overexpression of a receptortyrosine kinase; (2) benign and malignant cells of other proliferativediseases in which aberrant tyrosine kinase activation occurs; (4) anytumors that proliferate by receptor tyrosine kinases; (5) any tumorsthat proliferate by aberrant serine/threonine kinase activation; and (6)benign and malignant cells of other proliferative diseases in whichaberrant serine/threonine kinase activation occurs.

The term “treating” as used herein, unless otherwise indicated, meansreversing, alleviating, inhibiting the progress of, or preventing,either partially or completely, the growth of tumors, tumor metastases,or other cancer-causing or neoplastic cells in a patient. The term“treatment” as used herein, unless otherwise indicated, refers to theact of treating.

The phrase “a method of treating” or its equivalent, when applied to,for example, cancer refers to a procedure or course of action that isdesigned to reduce or eliminate the number of cancer cells in an animal,or to alleviate the symptoms of a cancer. “A method of treating” canceror another proliferative disorder does not necessarily mean that thecancer cells or other disorder will, in fact, be eliminated, that thenumber of cells or disorder will, in fact, be reduced, or that thesymptoms of a cancer or other disorder will, in fact, be alleviated.Often, a method of treating cancer will be performed even with a lowlikelihood of success, but which, given the medical history andestimated survival expectancy of an animal, is nevertheless deemed anoverall beneficial course of action.

The term “therapeutically effective agent” means a composition that willelicit the biological or medical response of a tissue, system, animal orhuman that is being sought by the researcher, veterinarian, medicaldoctor or other clinician.

The term “therapeutically effective amount” or “effective amount” meansthe amount of the subject compound or combination that will elicit thebiological or medical response of a tissue, system, animal or human thatis being sought by the researcher, veterinarian, medical doctor or otherclinician.

The data presented in the Examples herein below demonstrate that tumorcells, such as NSCLC or pancreatic cancer cells, containing wild typeEGFR, grown either in cell culture or in vivo, show a range ofsensitivities to inhibition by EGFR kinase inhibitors, dependent onwhether they have undergone an epithelial to mesenchymal transition(EMT). Prior to EMT, tumor cells are very sensitive to inhibition byEGFR kinase inhibitors such as erlotinib HCl (TARCEVA™), whereas tumorcells which have undergone an EMT are substantially less sensitive toinhibition by such compounds. The data indicates that the EMT may be a“general biological switch” that determines the level of sensitivity oftumors to EGFR kinase inhibitors. It is demonstrated that the level ofsensitivity of tumors to EGFR kinase inhibitors can be assessed bydetermining the level of biomarkers expressed by a tumor cell that arecharacteristic for cells either prior to or subsequent to an EMT event.For example, high levels of tumor cell expression of epithelialbiomarkers such as E-cadherin, indicative of a cell that has not yetundergone an EMT, correlate with high sensitivity to EGFR kinaseinhibitors. Conversely, high levels of tumor cell expression ofmesenchymal biomarkers such as vimentin or fibronectin, indicative of acell that has undergone an EMT, correlate with low sensitivity to EGFRkinase inhibitors. Thus, these observations can form the basis ofvaluable new diagnostic methods for predicting the effects of EGFRkinase inhibitors on tumor growth, and give oncologists an additionaltool to assist them in choosing the most appropriate treatment for theirpatients.

Accordingly, the present invention provides a method of predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, comprising: assessing the level of an epithelial biomarkerexpressed by a tumor cell; and predicting the sensitivity of tumor cellgrowth to inhibition by an EGFR kinase inhibitor, wherein highexpression levels of tumor cell epithelial biomarkers correlate withhigh sensitivity to inhibition by EGFR kinase inhibitors. Preferredexamples of epithelial biomarkers include E-cadherin and Brk (i.e.PTK-6) (see Table 1). Additional examples of epithelial biomarkers thatcan be utilized in the method of this invention include γ-catenin (i.e.junction plakoglobin), α-catenin (i.e. α1, α2, or α3 catenin), keratin8, keratin 18, connexin 31, plakophilin 3, stratafin 1, laminin alpha-5and ST14 (see Table 1).

The present invention also provides a method of predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, comprising: assessing the level of a mesenchymal biomarkerexpressed by a tumor cell; and predicting the sensitivity of tumor cellgrowth to inhibition by an EGFR kinase inhibitor, wherein highexpression levels of tumor cell mesenchymal biomarkers correlate withlow sensitivity to inhibition by EGFR kinase inhibitors. Preferredexamples of mesenchymal biomarkers include vimentin and fibronectin (seeTable 1). Additional examples of mesenchymal biomarkers that can beutilized in the method of this invention include fibrillin-1,fibrillin-2, collagen alpha-2(IV), collagen alpha-2(V), LOXL1, nidogen,C11orf9, tenascin, N-cadherin, and embryonal EDB⁺ fibronectin, tubulinalpha-3 and epimorphin (see Table 1).

In the practice of this invention, with preferred epithelial biomarkers,the level of expression in tumor cells that are sensitive to EGFR kinaseinhibitors will generally be at such a high level that the biomarkerwill be very readily detectable, using for example a specificanti-biomarker antibody for detection. With preferred epithelialbiomarkers, the level of expression in tumor cells that are relativelyinsensitive to EGFR kinase inhibitors will generally be at such a lowlevel that the biomarker will be barely detectable, if at all, usingsimilar procedures (e.g. in the data presented in the Examples hereinbelow, compare E-cadherin levels between sensitive and relativelyinsensitive tumor cells in FIGS. 2B, 3 and 5).

However, for other less preferred epithelial biomarkers, the level ofbiomarker expression in tumor cells that are relatively insensitive toEGFR kinase inhibitors may be readily detectable, but nevertheless willbe at a substantially lower level of expression than in tumor cells thatare sensitive to EGFR kinase inhibitors (e.g., in the data presented inthe Examples herein below, compare α-catenin levels for the relativelyinsensitive tumor cells H1703 or SW1573 with the sensitive tumor cellsH441, H358, H322 and H292 in FIG. 2B).

Similarly, in the practice of this invention, with preferred mesenchymalbiomarkers, the level of expression in tumor cells that are relativelyinsensitive to EGFR kinase inhibitors will generally be at such a highlevel that the biomarker will be very readily detectable, using forexample a specific anti-biomarker antibody for detection. With preferredmesenchymal biomarkers, the level of expression in tumor cells that arerelatively sensitive to EGFR kinase inhibitors will generally be at sucha low level that the biomarker will be barely detectable, if at all,using similar procedures (e.g. in the data presented in the Examplesherein below, compare fibronectin or vimentin levels between sensitiveand relatively insensitive tumor cells in FIGS. 2B, 3 and 5).

Also, for other less preferred mesenchymal biomarkers, the level ofbiomarker expression in tumor cells that are relatively sensitive toEGFR kinase inhibitors may be readily detectable, but nevertheless willbe at a substantially lower level of expression than in tumor cells thatare relatively insensitive to EGFR kinase inhibitors.

For any given epithelial or mesenchymal biomarker, the range ofexpression level between tumor cells that are relatively insensitive toEGFR kinase inhibitors and those that are sensitive, can readily beassessed by one of skill in the art, for example by testing on a panelof tumor cells as described herein (e.g. FIG. 2B), or by testing intumor biopsies from patients whose tumors display a range ofsensitivities to an EGFR kinase inhibitor (e.g. TARCEVA™).

In the context of this invention, for a relatively small percentage oftumor cells that are relatively insensitive to EGFR kinase inhibitors,the methods described above for predicting the sensitivity of tumor cellgrowth to inhibition by an EGFR kinase inhibitor, comprising assessingthe level of an epithelial or mesenchymal biomarker expressed by a tumorcell, in circumstances where only a single biomarker level is assessed,may falsely predict that tumor cell growth is sensitive to inhibition byan EGFR kinase inhibitor. For example, in the data presented in theExamples herein below, the levels of the epithelial biomarkers γ-cateninand α-catenin in H460 tumor cells, or the mesenchymal biomarkerfibronectin in H1703 cells, falsely predict high sensitivity to EGFRkinase inhibitors (see FIG. 2B). Thus, based on such false predictions,a physician may be lead to treat a small number of patients with EGFRkinase inhibitors, and the tumor may not be sensitive to the inhibitor.However, for the vast majority of tumor cells (e.g. at least 90%, fromthe data presented in the Examples herein below), assessment of a singlebiomarker expression level would be expected to provide an accurateprediction of level of sensitivity to EGFR kinase inhibitors.

Furthermore, most importantly in the context of this invention, no tumorcells that are sensitive to EGFR kinase inhibitors have been found thatwhen tested by the above methods (where only a single biomarker level isassessed) give a false prediction that tumor cell growth will beinsensitive to inhibition by an EGFR kinase inhibitor. Thus, utilizingthe testing methods described herein should never lead a physician towithhold treatment with an EGFR kinase inhibitor in cases where thepatient may benefit from such treatment.

In addition, one of skill in the medical arts, particularly pertainingto the application of diagnostic tests and treatment with therapeutics,will recognize that biological systems are somewhat variable and notalways entirely predictable, and thus many good diagnostic tests ortherapeutics are occasionally ineffective. Thus, it is ultimately up tothe judgement of the attending physician to determine the mostappropriate course of treatment for an individual patient, based upontest results, patient condition and history, and his own experience.There may even be occasions, for example, when a physician will chooseto treat a patient with an EGFR kinase inhibitor even when a tumor isnot predicted to be particularly sensitive to EGFR kinase inhibitors,based on data from diagnostic tests or from other criteria, particularlyif all or most of the other obvious treatment options have failed, or ifsome synergy is anticipated when given with another treatment. The factthat the EGFR kinase inhibitors as a class of drugs are relatively welltolerated compared to many other anti-cancer drugs, such as moretraditional chemotherapy or cytotoxic agents used in the treatment ofcancer, makes this a more viable option.

Preferred examples of suitable epithelial biomarkers for use in thisinvention, such as E-cadherin, do not lead to any false predictions whenused in the methods described above (where only a single biomarker levelis assessed).

Furthermore, this invention also provides additional methods whereinsimultaneous assessment of the expression level in tumor cells of morethan one biomarker level is utilized. In preferred embodiments of thesemethods (described below) there is no level of false prediction, as isthe case for some of the methods described above where a singlebiomarker expression level is assessed.

Accordingly, the present invention provides a method of predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, comprising: assessing the level of one or more (or a panelof) epithelial biomarkers expressed by a tumor cell; and predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, wherein simultaneous high expression levels of all of thetumor cell epithelial biomarkers correlates with high sensitivity toinhibition by EGFR kinase inhibitors. In one preferred embodiment ofthis method the epithelial biomarkers comprise E-cadherin and Brk,wherein simultaneous high expression level of the two tumor cellepithelial biomarkers correlates with high sensitivity to inhibition byEGFR kinase inhibitor. In another preferred embodiment of this methodthe epithelial biomarkers comprise E-cadherin and γ-catenin, whereinsimultaneous high expression level of the two tumor cell epithelialbiomarkers correlates with high sensitivity to inhibition by EGFR kinaseinhibitor. Note that in the two latter preferred embodiments a highexpression level of both biomarkers is required to indicate highsensitivity.

The present invention also provides a method of predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, comprising: assessing the level of one or more (or a panelof) mesenchymal biomarkers expressed by a tumor cell; and predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, wherein simultaneous low or undetectable expression levels ofall of the tumor cell mesenchymal biomarkers correlates with highsensitivity to inhibition by EGFR kinase inhibitors. In one preferredembodiment of this method the mesenchymal biomarkers comprise vimentinand fibronectin, wherein simultaneous low or undetectable expressionlevel of the two tumor cell mesenchymal biomarkers correlates with highsensitivity to inhibition by EGFR kinase inhibitor. Note that in thelatter preferred embodiment a low or undetectable expression of bothbiomarkers is required to indicate high sensitivity.

The present invention also provides a method of predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, comprising: assessing the level of an epithelial biomarkerexpressed by a tumor cell; assessing the level of a mesenchymalbiomarker expressed by a tumor cell; and predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor, wherein ahigh ratio of epithelial to mesenchymal biomarker expression levelscorrelates with high sensitivity to inhibition by EGFR kinaseinhibitors. In one preferred embodiment of this method the epithelialbiomarker comprises E-cadherin and the mesenchymal biomarker comprisesfibronectin. In another preferred embodiment of this method theepithelial biomarker comprises Brk and the mesenchymal biomarkercomprises fibronectin. In another preferred embodiment of this methodthe epithelial biomarker comprises E-cadherin and the mesenchymalbiomarker comprises vimentin. In another preferred embodiment of thismethod the epithelial biomarker comprises γ-catenin and the mesenchymalbiomarker comprises fibronectin.

The present invention also provides a method of predicting thesensitivity of tumor growth to inhibition by an EGFR kinase inhibitor,comprising: assessing the level of one or more (or a panel of)epithelial biomarkers expressed by cells of the tumor; and predictingthe sensitivity of tumor growth to inhibition by an EGFR kinaseinhibitor, wherein simultaneous high expression levels of all of thetumor cell epithelial biomarkers correlates with high sensitivity toinhibition by EGFR kinase inhibitors. In one preferred embodiment ofthis method the epithelial biomarkers comprise E-cadherin and Brk,wherein simultaneous high expression level of the two tumor cellepithelial biomarkers correlates with high sensitivity to inhibition byEGFR kinase inhibitor. In another preferred embodiment of this methodthe epithelial biomarkers comprise E-cadherin and γ-catenin, whereinsimultaneous high expression level of the two tumor cell epithelialbiomarkers correlates with high sensitivity to inhibition by EGFR kinaseinhibitor. Note that in the two latter preferred embodiments a highexpression level of both biomarkers is required to indicate highsensitivity.

The present invention also provides a method of predicting thesensitivity of tumor growth to inhibition by an EGFR kinase inhibitor,comprising: assessing the level of one or more (or a panel of)mesenchymal biomarkers expressed by cells of the tumor; and predictingthe sensitivity of tumor growth to inhibition by an EGFR kinaseinhibitor, wherein simultaneous low or undetectable expression levels ofall of the tumor cell mesenchymal biomarkers correlates with highsensitivity to inhibition by EGFR kinase inhibitors. In one preferredembodiment of this method the mesenchymal biomarkers comprise vimentinand fibronectin, wherein simultaneous low or undetectable expressionlevel of the two tumor cell mesenchymal biomarkers correlates with highsensitivity to inhibition by EGFR kinase inhibitor. Note that in thelatter preferred embodiment a low or undetectable expression of bothbiomarkers is required to indicate high sensitivity.

The present invention also provides a method of predicting thesensitivity of tumor growth to inhibition by an EGFR kinase inhibitor,comprising: assessing the level of an epithelial biomarker expressed bycells of the tumor; assessing the level of a mesenchymal biomarkerexpressed by cells of the tumor; and predicting the sensitivity of tumorgrowth to inhibition by an EGFR kinase inhibitor, wherein a high ratioof epithelial to mesenchymal biomarker expression levels correlates withhigh sensitivity to inhibition by EGFR kinase inhibitors. In onepreferred embodiment of this method the epithelial biomarker comprisesE-cadherin and the mesenchymal biomarker comprises fibronectin. Inanother preferred embodiment of this method the epithelial biomarkercomprises Brk and the mesenchymal biomarker comprises fibronectin. Inanother preferred embodiment of this method the epithelial biomarkercomprises E-cadherin and the mesenchymal biomarker comprises vimentin.In another preferred embodiment of this method the epithelial biomarkercomprises γ-catenin and the mesenchymal biomarker comprises fibronectin.

The present invention also provides a method of predicting whether acancer patient is afflicted with a tumor that will respond effectivelyto treatment with an EGFR kinase inhibitor, comprising: assessing thelevel of one or more (or a panel of) epithelial biomarkers expressed bycells of the tumor; and predicting if the tumor will respond effectivelyto treatment with an EGFR kinase inhibitor, wherein simultaneous highexpression levels of all of the tumor cell epithelial biomarkerscorrelates with a tumor that will respond effectively to treatment withan EGFR kinase inhibitor. In one preferred embodiment of this method theepithelial biomarkers comprise E-cadherin and Brk, wherein simultaneoushigh expression level of the two tumor cell epithelial biomarkerscorrelates with a tumor that will respond effectively to treatment withan EGFR kinase inhibitor. In another preferred embodiment of this methodthe epithelial biomarkers comprise E-cadherin and γ-catenin, whereinsimultaneous high expression level of the two tumor cell epithelialbiomarkers correlates with a tumor that will respond effectively totreatment with an EGFR kinase inhibitor. Note that in the two latterpreferred embodiments a high expression level of both biomarkers isrequired to indicate a tumor that will respond effectively to treatmentwith an EGFR kinase inhibitor.

The present invention also provides a method of predicting whether acancer patient is afflicted with a tumor that will respond effectivelyto treatment with an EGFR kinase inhibitor, comprising: assessing thelevel of one or more (or a panel of) mesenchymal biomarkers expressed bycells of the tumor; and predicting if the tumor will respond effectivelyto treatment with an EGFR kinase inhibitor, wherein simultaneous low orundetectable expression levels of all of the tumor cell mesenchymalbiomarkers correlates with a tumor that will respond effectively totreatment with an EGFR kinase inhibitor. In one preferred embodiment ofthis method the mesenchymal biomarkers comprise vimentin andfibronectin, wherein simultaneous low or undetectable expression levelof the two tumor cell mesenchymal biomarkers correlates with a tumorthat will respond effectively to treatment with an EGFR kinaseinhibitor. Note that in the latter preferred embodiment a low orundetectable expression of both biomarkers is required to indicate atumor that will respond effectively to treatment with an EGFR kinaseinhibitor.

The present invention also provides a method of predicting whether acancer patient is afflicted with a tumor that will respond effectivelyto treatment with an EGFR kinase inhibitor, comprising: assessing thelevel of an epithelial biomarker expressed by cells of the tumor;assessing the level of a mesenchymal biomarker expressed by cells of thetumor; and predicting if the tumor will respond effectively to treatmentwith an EGFR kinase inhibitor, wherein a high ratio of epithelial tomesenchymal biomarker expression levels correlates with a tumor thatwill respond effectively to treatment with an EGFR kinase inhibitor. Inone preferred embodiment of this method the epithelial biomarkercomprises E-cadherin and the mesenchymal biomarker comprisesfibronectin. In another preferred embodiment of this method theepithelial biomarker comprises Brk and the mesenchymal biomarkercomprises fibronectin. In another preferred embodiment of this methodthe epithelial biomarker comprises E-cadherin and the mesenchymalbiomarker comprises vimentin. In another preferred embodiment of thismethod the epithelial biomarker comprises γ-catenin and the mesenchymalbiomarker comprises fibronectin.

In the context of the methods of this invention, biomarkers expressed bya tumor cell can include molecular and cellular markers that indicatethe transition state of the tumor cell. In a preferred embodiment thebiomarker is an individual marker protein, or its encoding mRNA,characteristic of the particular transition state of the tumor, i.e. atumor exhibiting epithelial or mesenchymal characteristics. In analternative embodiment, in certain circumstances the biomarker may be acharacteristic morphological pattern produced in the tumor cell bycellular macromolecules that is characteristic of either an epithelialor mesenchymal condition. TABLE 1 Molecular Biomarker GeneIdentification Human Biomarker NCBI GeneID¹ NCBI RefSeq² E-cadherin 999NP_004351 Brk 5753 NP_005966 γ-catenin 3728 NP_002221 α1-catenin 1495NP_001894 α2-catenin 1496 NP_004380 α3-catenin 29119 NP_037398 keratin 83856 NP_002264 keratin 18 3875 NP_000215 connexin 31 2707 NP_076872plakophilin 3 11187 NP_009114 stratifin 1 2810 NP_006133 laminin alpha-53911 NP_005551 ST14 19143 NP_035306 vimentin 7431 NP_003371 fibronectin1 2335 NP_002017 fibrillin-1 2200 NP_000129 fibrillin-2 2201 NP_001990collagen alpha2(IV) 1284 NP_001837 collagen alpha2(V) 1290 NP_000384LOXL1 4016 NP_005567 nidogen 4811 NP_002499 C11orf9 745 NP_037411tenascin 3371 NP_002151 N-cadherin 1000 NP_001783 tubulin alpha-3 7846NP_006009 epimorphin 2054 NP_919337¹The NCBI GeneID number is a unique identifier of the biomarker genefrom the NCBI Entrez Gene database record (National Center forBiotechnology Information (NCBI), U.S. National Library of Medicine,8600 Rockville Pike, Building 38A, Bethesda, MD 20894; Internet addresshttp://www.ncbi.nlm.nih.gov/).²The NCBI RefSeq (Reference Sequence) is an example of a sequenceexpressed by the biomarker gene.

Table 1 lists the genes coding for examples of molecular biomarkers thatcan be used in the practice of the methods of the invention describedherein. The molecular biomarkers can include any product expressed bythese genes, including variants thereof, e.g. expressed MRNA or protein,splice variants, co- and post-translationally modified proteins,polymorphic variants etc. In one embodiment the biomarker is theembryonal EDB⁺ fibronectin, a splice variant expressed by thefibronectin 1 gene (Kilian, 0. et al. (2004) Bone 35(6):1334-1345). Apossible advantage of determining this fetal form of fibronectin is thatone could readily distinguish mesenchymal-like tumors from surroundingstromal tissue. In an additional embodiment the biomarker can be ananimal homologue of the human gene product (e.g. from dog, mouse, rat,rabbit, cat, monkey, ape, etc.).

In the methods described herein the tumor cell will typically be from apatient diagnosed with cancer, a precancerous condition, or another formof abnormal cell growth, and in need of treatment. The cancer may belung cancer (e.g. non-small cell lung cancer (NSCLC)), pancreaticcancer, head and neck cancer, gastric cancer, breast cancer, coloncancer, ovarian cancer, or any of a variety of other cancers describedherein below. The cancer is preferably one known to be potentiallytreatable with an EGFR kinase inhibitor.

In the methods of this invention, biomarker expression level can beassessed relative to a control molecule whose expression level remainsconstant throughout EMT, or when comparing tumor cells expressing eitherepithelial or mesenchymal transition states as indicated by molecularbiomarkers (e.g. a “housekeeping” gene, such as GAPDH, β-actin, tubulin,or the like). Biomarker expression level can also be assessed relativeto the other type of tumor cell biomarker (i.e. epithelial compared tomesenchymal), or to the biomarker level in non-tumor cells of the sametissue, or another cell or tissue source used as an assay reference.

In the methods of this invention, the level of an epithelial ormesenchymal biomarker expressed by a tumor cell can be assessed by usingany of the standard bioassay procedures known in the art fordetermination of the level of expression of a gene, including forexample ELISA, RIA, immunopreciptation, immunoblotting,immunofluorescence microscopy, RT-PCR, in situ hybridization, cDNAmicroarray, or the like, as described in more detail below.

In the methods of this invention, the expression level of a tumor cellepithelial or mesenchymal biomarker is preferably assessed by assaying atumor biopsy. However, in an alternative embodiment, expression level ofthe tumor cell biomarker can be assessed in bodily fluids or excretionscontaining detectable levels of biomarkers originating from the tumor ortumor cells. Bodily fluids or excretions useful in the present inventioninclude blood, urine, saliva, stool, pleural fluid, lymphatic fluid,sputum, ascites, prostatic fluid, cerebrospinal fluid (CSF), or anyother bodily secretion or derivative thereof. By blood it is meant toinclude whole blood, plasma, serum or any derivative of blood.Assessment of tumor epithelial or mesenchymal biomarkers in such bodilyfluids or excretions can sometimes be preferred in circumstances wherean invasive sampling method is inappropriate or inconvenient.

In the methods of this invention, the tumor cell can be a lung cancertumor cell (e.g. non-small cell lung cancer (NSCLC)), a pancreaticcancer tumor cell, a breast cancer tumor cell, a head and neck cancertumor cell, a gastric cancer tumor cell, a colon cancer tumor cell, anovarian cancer tumor cell, or a tumor cell from any of a variety ofother cancers as described herein below. The tumor cell is preferably ofa type known to or expected to express EGFR kinase, as do all tumorcells from solid tumors. The EGFR kinase can be wild type or a mutantform.

In the methods of this invention, the EGFR kinase inhibitor can be anyEGFR kinase inhibitor as described herein below, but is preferably6,7-bis(2-methoxyethoxy)-4-quinazolin-4-yl]-(3-ethynylphenyl) amine(also known as erlotinib, OSI-774, or TARCEVA™ (erlotinib HCl),including pharmacologically acceptable salts or polymorphs thereof.

The following methods represent additional specific embodiments of themethod of the invention.

The present invention provides a method of predicting the sensitivity oftumor growth to inhibition by an EGFR kinase inhibitor, comprising:assessing the level of an epithelial biomarker expressed by cells of thetumor; and predicting the sensitivity of tumor growth to inhibition byan EGFR kinase inhibitor, wherein high expression levels of tumor cellepithelial biomarkers correlate with high sensitivity of tumor growth toinhibition by EGFR kinase inhibitors.

The present invention provides a method of predicting the sensitivity oftumor growth to inhibition by an EGFR kinase inhibitor, comprising:assessing the level of a mesenchymal biomarker expressed by cells of thetumor; and predicting the sensitivity of tumor growth to inhibition byan EGFR kinase inhibitor, wherein high expression levels of tumor cellmesenchymal biomarkers correlate with low sensitivity of tumor growth toinhibition by EGFR kinase inhibitors.

The present invention provides a method of predicting whether a cancerpatient is afflicted with a tumor that will respond effectively totreatment with an EGFR kinase inhibitor, comprising: assessing the levelof an epithelial biomarker expressed by cells of the tumor; andpredicting if the tumor will respond effectively to treatment with anEGFR kinase inhibitor, wherein high expression levels of tumor cellepithelial biomarkers correlate with a tumor that will respondeffectively to treatment with an EGFR kinase inhibitor.

In the methods of this invention, the tumor can be a lung cancer tumor(e.g. non-small cell lung cancer (NSCLC)), a pancreatic cancer tumor, abreast cancer tumor, a head and neck cancer tumor, a gastric cancertumor, a colon cancer tumor, an ovarian cancer tumor, or a tumor fromany of a variety of other cancers as described herein below. The tumoris preferably of a type whose cells are known to or expected to expressEGFR kinase, as do all solid tumors. The EGFR kinase can be wild type ora mutant form.

The present invention provides a method of predicting whether a cancerpatient is afflicted with a tumor that will respond effectively totreatment with an EGFR kinase inhibitor, comprising: assessing the levelof a mesenchymal biomarker expressed by cells of the tumor; andpredicting if the tumor will respond effectively to treatment with anEGFR kinase inhibitor, wherein high expression levels of tumor cellmesenchymal biomarkers correlate with a tumor that will respond lesseffectively to treatment with an EGFR kinase inhibitor.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one epithelial biomarkerpolypeptide; determining the tumor cell level of at least one controlpolypeptide; comparing the tumor cell level of at least one epithelialbiomarker polypeptide to the tumor cell level of at least one controlpolypeptide; wherein a high ratio of tumor cell biomarker polypeptide totumor cell control polypeptide indicates a high predicted sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor. For thismethod, examples of useful epithelial biomarker polypeptides includeE-cadherin, γ-catenin, keratin 8, keratin 18, connexin 31, plakophilin3, stratafin 1, laminin alpha-5, ST14 and Brk.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one epithelial biomarkerpolynucleotide that encodes an polypeptide; determining the tumor celllevel of at least one control polynucleotide; comparing the tumor celllevel of at least one epithelial biomarker polynucleotide that encodes apolypeptide to the tumor cell level of at least one controlpolynucleotide; wherein a high ratio of tumor cell biomarkerpolynucleotide to tumor cell control polynucleotide indicates a highpredicted sensitivity of tumor cell growth to inhibition by an EGFRkinase inhibitor. For this method examples of polypeptides encoded bythe epithelial biomarker polynucleotide include E-cadherin, γ-catenin,keratin 8, keratin 18, connexin 31, plakophilin 3, stratafin 1, lamininalpha-5, ST14 and Brk.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one mesenchymal biomarkerpolypeptide; determining the tumor cell level of at least one controlpolypeptide; comparing the tumor cell level of at least one mesenchymalbiomarker polypeptide to the tumor cell level of at least one controlpolypeptide; wherein a low ratio of tumor cell biomarker polypeptide totumor cell control polypeptide indicates a high predicted sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor. For thismethod, examples of useful mesenchymal biomarker polypeptides includevimentin and fibronectin.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one mesenchymal biomarkerpolynucleotide that encodes an polypeptide; determining the tumor celllevel of at least one control polynucleotide; comparing the tumor celllevel of at least one mesenchymal biomarker polynucleotide that encodesan polypeptide to the tumor cell level of at least one controlpolynucleotide; wherein a low ratio of tumor cell biomarkerpolynucleotide to tumor cell control polynucleotide indicates a highpredicted sensitivity of tumor cell growth to inhibition by an EGFRkinase inhibitor. For this method, examples of useful polypeptidesencoded by the biomarker polynucleotide include vimentin andfibronectin.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one epithelial biomarkerpolypeptide; determining a non-tumor cell level of at least oneepithelial biomarker polypeptide; comparing the tumor cell level of atleast one epithelial biomarker polypeptide to the non-tumor cell levelof at least one epithelial biomarker polypeptide; wherein a high ratioof tumor cell biomarker polypeptide to non-tumor cell biomarkerpolypeptide indicates a high predicted sensitivity of tumor cell growthto inhibition by an EGFR kinase inhibitor. For this method, examples ofuseful epithelial biomarker polypeptide include E-cadherin, γ-catenin,keratin 8, keratin 18, connexin 31, plakophilin 3, stratafin 1, lamininalpha-5, ST14 and Brk.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one epithelial biomarkerpolynucleotide that encodes an polypeptide; determining a non-tumor celllevel of at least one epithelial biomarker polynucleotide that encodesan polypeptide; comparing the tumor cell level of at least oneepithelial biomarker polynucleotide that encodes an polypeptide to thenon-tumor cell level of at least one epithelial biomarker polynucleotidethat encodes an polypeptide; wherein a high ratio of tumor cellbiomarker polynucleotide to non-tumor cell biomarker polynucleotideindicates a high predicted sensitivity of tumor cell growth toinhibition by an EGFR kinase inhibitor. For this method, examples ofuseful polypeptides encoded by the epithelial biomarker polynucleotideinclude E-cadherin, γ-catenin, keratin 8, keratin 18, connexin 31,plakophilin 3, stratafin 1, laminin alpha-5, ST14 and Brk.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one mesenchymal biomarkerpolypeptide; determining a non-tumor cell level of at least onemesenchymal biomarker polypeptide; comparing the tumor cell level of atleast one mesenchymal biomarker polypeptide to the non-tumor cell levelof at least one mesenchymal biomarker polypeptide; wherein a low ratioof tumor cell biomarker polypeptide to non-tumor cell biomarkerpolypeptide indicates a high predicted sensitivity of tumor cell growthto inhibition by an EGFR kinase inhibitor. For this method, examples ofuseful mesenchymal biomarker polypeptides include vimentin andfibronectin.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one mesenchymal biomarkerpolynucleotide that encodes an polypeptide; determining a non-tumor celllevel of at least one mesenchymal biomarker polynucleotide that encodesan polypeptide; comparing the tumor cell level of at least onemesenchymal biomarker polynucleotide that encodes an polypeptide to thenon-tumor cell level of at least one mesenchymal biomarkerpolynucleotide that encodes an polypeptide; wherein a low ratio of tumorcell biomarker polynucleotide to non-tumor cell biomarker polynucleotideindicates a high predicted sensitivity of tumor cell growth toinhibition by an EGFR kinase inhibitor. For this method, examples ofuseful polypeptides encoded by the biomarker polynucleotide includevimentin and fibronectin.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one epithelial biomarkerpolypeptide; determining the tumor cell level of at least onemesenchymal biomarker polypeptide; comparing the level of at least oneepithelial biomarker polypeptide to the level of at least onemesenchymal biomarker polypeptide; wherein a high ratio of epithelialbiomarker polypeptide to mesenchymal biomarker polypeptide indicates ahigh predicted sensitivity of tumor cell growth to inhibition by an EGFRkinase inhibitor. For this method, examples of useful epithelialbiomarker polypeptides include E-cadherin, γ-catenin, keratin 8, keratin18, connexin 31, plakophilin 3, stratafin 1, laminin alpha-5, ST14 andBrk. For this method, examples of useful mesenchymal biomarkerpolypeptides include vimentin and fibronectin.

The present invention provides a method of predicting the sensitivity oftumor cell growth to inhibition by an EGFR kinase inhibitor comprising:determining the tumor cell level of at least one epithelial biomarkerpolynucleotide that encodes a polypeptide; determining the tumor celllevel of at least one mesenchymal biomarker polynucleotide that encodesa polypeptide; (c) comparing the level of at least one epithelialbiomarker polynucleotide to the level of at least one mesenchymalbiomarker polynucleotide; wherein a high ratio of epithelial biomarkerpolynucleotide to mesenchymal biomarker polynucleotide indicates apredicted high sensitivity of tumor cell growth to inhibition by an EGFRkinase inhibitor. For this method, examples of useful polypeptidesencoded by the epithelial biomarker polynucleotide include E-cadherin,γ-catenin, keratin 8, keratin 18, connexin 31, plakophilin 3, stratafin1, laminin alpha-5, ST14 and Brk. For this method, examples of usefulpolypeptides encoded by the mesenchymal biomarker polynucleotide includevimentin and fibronectin.

The present invention provides a method of assessing whether a cancerpatient is afflicted with a cancer that will respond effectively totreatment with an EGFR kinase inhibitor, the method comprisingcomparing: the level of expression of a mesenchymal biomarker in apatient sample; and the normal level of expression of the biomarker in acontrol non-cancer sample, wherein a significant increase in the levelof expression of the mesenchymal biomarker in the patient sample overthe normal level is an indication that the patient is afflicted with acancer which is less likely to respond effectively to treatment with anEGFR kinase inhibitor. For this method, examples of useful mesenchymalbiomarkers include vimentin and fibronectin, and nucleic acids encodingfor these proteins.

The present invention provides a method of assessing whether a cancerpatient is afflicted with a cancer that will respond effectively totreatment with an EGFR kinase inhibitor, the method comprisingcomparing: the level of expression of an epithelial biomarker in apatient sample; and the normal level of expression of the biomarker in acontrol non-cancer sample, wherein a significant decrease in the levelof expression of the epithelial biomarker in the patient sample over thenormal level is an indication that the patient is afflicted with acancer which is less likely to respond effectively to treatment with anEGFR kinase inhibitor. For this method, examples of useful epithelialbiomarkers include E-cadherin, γ-catenin, keratin 8, keratin 18,connexin 31, plakophilin 3, stratafin 1, laminin alpha-5, ST14 and Brk,and nucleic acids encoding for these proteins.

The present invention provides a method of assessing whether a cancerpatient is afflicted with a cancer that will respond effectively totreatment with an EGFR kinase inhibitor, the method comprisingcomparing: the level of expression of an epithelial biomarker in apatient sample; and the level of expression of a mesenchymal biomarkerin a patient sample, wherein a high ratio of the level of expression ofthe epithelial biomarker to the level of expression of the mesenchymalbiomarker is an indication that the patient is afflicted with a cancerwhich is likely to respond effectively to treatment with an EGFR kinaseinhibitor. For this method, examples of useful epithelial biomarkersinclude E-cadherin, γ-catenin, keratin 8, keratin 18, connexin 31,plakophilin 3, stratafin 1, laminin alpha-5, ST14 and Brk, and nucleicacids encoding for these proteins. For this method, examples of usefulmesenchymal biomarkers include vimentin and fibronectin, and nucleicacids encoding for these proteins.

In any of the above methods referring to a patient sample, an example ofsuch a sample can be a tumor biopsy.

The present invention provides a method of determining whether in ahuman subject a tumor will be responsive to treatment with an EGFRkinase inhibitor, comprising: (a) collecting a sample of a bodilysubstance containing human nucleic acid or protein, said nucleic acid orprotein having originated from cells of the human subject, (b)determining quantitatively or semi-quantitatively in the sample a levelof expression for one or more epithelial cell biomarker proteins or oneor more epithelial cell biomarker protein-specific mRNAs; and (c)comparing the expression level in (b) to the level of biomarkerexpression in a normal control, or to the level of a control polypeptideor nucleic acid in the sample, wherein reduced expression of one or moreepithelial cell biomarker proteins or one or more epithelial cellbiomarker protein-specific mRNAs, with respect to the control level,indicates the presence in the human subject of a tumor which is lesslikely to respond effectively to treatment with an EGFR kinaseinhibitor.

The present invention provides a method of determining whether in ahuman subject a tumor will be responsive to treatment with an EGFRkinase inhibitor, comprising: (a) collecting a sample of a bodilysubstance containing human nucleic acid or protein, said nucleic acid orprotein having originated from cells of the human subject, (b)determining quantitatively or semi-quantitatively in the sample a levelof expression for one or more mesenchymal cell biomarker proteins or oneor more mesenchymal cell biomarker protein-specific mRNAs; and (c)comparing the expression level in (b) to the level of biomarkerexpression in a normal control, or to the level of a control polypeptideor nucleic acid in the sample, wherein increased expression of one ormore mesenchymal cell biomarker proteins or one or more mesenchymal cellbiomarker protein-specific mRNAs, with respect to the control level,indicates the presence in the human subject of a tumor which is lesslikely to respond effectively to treatment with an EGFR kinaseinhibitor.

The present invention provides a method of determining the likelihoodthat a patient with a tumor will show relatively long survival benefitfrom therapy with an EGFR kinase inhibitor, comprising determining thelevel of one or more epithelial biomarkers in the cells of the tumor,comparing said level with the level of epithelial biomarker expressionin a non-tumor control, or to the level of a control polypeptide ornucleic acid in the tumor sample, and determining whether the cells ofthe tumor contain a relatively high level of one or more epithelialbiomarkers, a high level being indicative that a patient with a tumorwill show relatively long survival benefit from therapy with an EGFRkinase inhibitor.

The present invention provides a method of determining the likelihoodthat a patient with a tumor will show relatively long survival benefitfrom therapy with an EGFR kinase inhibitor, comprising determining thelevel of one or more mesenchymal biomarkers in the cells of the tumor,comparing said level with the level of mesenchymal biomarker expressionin a non-tumor control, or to the level of a control polypeptide ornucleic acid in the tumor sample, and determining whether the cells ofthe tumor contain a relatively low level of one or more mesenchymalbiomarkers, a low level being indicative that a patient with a tumorwill show relatively long survival benefit from therapy with an EGFRkinase inhibitor.

The present invention provides a method for determining for a patientwith a tumor the likelihood that said patient will show relatively longsurvival benefit from therapy with an EGFR kinase inhibitor, comprising:determining the level of one or more epithelial biomarkers in the cellsof the tumor, comparing said level with the level of epithelialbiomarker expression in a non-tumor control, or to the level of acontrol polypeptide or nucleic acid in the tumor sample, and determiningwhether the cells of the tumor contain a relatively high level of one ormore epithelial biomarkers; determining the level of one or moremesenchymal biomarkers in the cells of the tumor, comparing said levelwith the level of mesenchymal biomarker expression in a non-tumorcontrol, or to the level of a control polypeptide or nucleic acid in thetumor sample, and determining whether the cells of the tumor contain arelatively low level of one or more mesenchymal biomarkers, wherein ahigh level of one or more epithelial biomarkers and a low level of oneor more mesenchymal biomarkers is indicative that a patient with a tumorwill show relatively long survival benefit from therapy with an EGFRkinase inhibitor.

The present invention provides a method of determining a prognosis forsurvival for a patient with a neoplastic condition in response totherapy with an EGFR kinase inhibitor, comprising: measuring the levelof an epithelial biomarker associated with neoplastic cells, andcomparing said level of epithelial biomarker to a non-neoplasticepithelial biomarker reference level, or to the level of a controlpolypeptide or nucleic acid associated with the neoplastic cells,wherein a decreased level of epithelial biomarker associated with theneoplastic cells correlates with decreased survival of said patient.

The present invention provides a method of determining a prognosis forsurvival for a patient with a neoplastic condition in response totherapy with an EGFR kinase inhibitor, comprising: measuring the levelof an mesenchymal biomarker associated with neoplastic cells, andcomparing said level of mesenchymal biomarker to a non-neoplasticmesenchymal biomarker reference level, or to the level of a controlpolypeptide or nucleic acid associated with the neoplastic cells,wherein an increased level of mesenchymal biomarker associated with theneoplastic cells correlates with decreased survival of said patient.

For assessment of tumor cell epithelial or mesenchymal biomarkerexpression, patient samples containing tumor cells, or proteins ornucleic acids produced by these tumor cells, may be used in the methodsof the present invention. In these embodiments, the level of expressionof the biomarker can be assessed by assessing the amount (e.g. absoluteamount or concentration) of the marker in a tumor cell sample, e.g., atumor biopsy obtained from a patient, or other patient sample containingmaterial derived from the tumor (e.g. blood, serum, urine, or otherbodily fluids or excretions as described herein above). The cell samplecan, of course, be subjected to a variety of well-known post-collectionpreparative and storage techniques (e.g., nucleic acid and/or proteinextraction, fixation, storage, freezing, ultrafiltration, concentration,evaporation, centrifugation, etc.) prior to assessing the amount of themarker in the sample. Likewise, tumor biopsies may also be subjected topost-collection preparative and storage techniques, e.g., fixation.

In the methods of the invention, one can detect expression of biomarkerproteins having at least one portion which is displayed on the surfaceof tumor cells which express it. It is a simple matter for the skilledartisan to determine whether a marker protein, or a portion thereof, isexposed on the cell surface. For example, immunological methods may beused to detect such proteins on whole cells, or well knowncomputer-based sequence analysis methods may be used to predict thepresence of at least one extracellular domain (i.e. including bothsecreted proteins and proteins having at least one cell-surface domain).Expression of a marker protein having at least one portion which isdisplayed on the surface of a cell which expresses it may be detectedwithout necessarily lysing the tumor cell (e.g. using a labeled antibodywhich binds specifically with a cell-surface domain of the protein).

Expression of a biomarkers described in this invention may be assessedby any of a wide variety of well known methods for detecting expressionof a transcribed nucleic acid or protein. Non-limiting examples of suchmethods include immunological methods for detection of secreted,cell-surface, cytoplasmic, or nuclear proteins, protein purificationmethods, protein function or activity assays, nucleic acid hybridizationmethods, nucleic acid reverse transcription methods, and nucleic acidamplification methods.

In one embodiment, expression of a biomarker is assessed using anantibody (e.g. a radio-labeled, chromophore-labeled,fluorophore-labeled, or enzyme-labeled antibody), an antibody derivative(e.g. an antibody conjugated with a substrate or with the protein orligand of a protein-ligand pair {e.g. biotin-streptavidin}), or anantibody fragment (e.g. a single-chain antibody, an isolated antibodyhypervariable domain, etc.) which binds specifically with a biomarkerprotein or fragment thereof, including a biomarker protein which hasundergone either all or a portion of post-translational modifications towhich it is normally subjected in the tumor cell (e.g. glycosylation,phosphorylation, methylation etc.).

In another embodiment, expression of a biomarker is assessed bypreparing mRNA/cDNA (i.e. a transcribed polynucleotide) from cells in apatient sample, and by hybridizing the mRNA/cDNA with a referencepolynucleotide which is a complement of a biomarker nucleic acid, or afragment thereof. cDNA can, optionally, be amplified using any of avariety of polymerase chain reaction methods prior to hybridization withthe reference polynucleotide. Expression of one or more biomarkers canlikewise be detected using quantitative PCR to assess the level ofexpression of the biomarker(s). Alternatively, any of the many knownmethods of detecting mutations or variants (e.g. single nucleotidepolymorphisms, deletions, etc.) of a biomarker of the invention may beused to detect occurrence of a biomarker in a patient.

In a related embodiment, a mixture of transcribed polynucleotidesobtained from the sample is contacted with a substrate having fixedthereto a polynucleotide complementary to or homologous with at least aportion (e.g. at least 7, 10, 15, 20, 25, 30, 40, 50, 100, 500, or morenucleotide residues) of a biomarker nucleic acid. If polynucleotidescomplementary to or homologous with are differentially detectable on thesubstrate (e.g. detectable using different chromophores or fluorophores,or fixed to different selected positions), then the levels of expressionof a plurality of biomarkers can be assessed simultaneously using asingle substrate (e.g. a “gene chip” microarray of polynucleotides fixedat selected positions). When a method of assessing biomarker expressionis used which involves hybridization of one nucleic acid with another,it is preferred that the hybridization be performed under stringenthybridization conditions.

When a plurality of biomarkers of the invention are used in the methodsof the invention, the level of expression of each biomarker in a patientsample can be compared with the normal level of expression of each ofthe plurality of biomarkers in non-cancerous samples of the same type,either in a single reaction mixture (i.e. using reagents, such asdifferent fluorescent probes, for each biomarker) or in individualreaction mixtures corresponding to one or more of the biomarkers.

The level of expression of a biomarker in normal (i.e. non-cancerous)human tissue can be assessed in a variety of ways. In one embodiment,this normal level of expression is assessed by assessing the level ofexpression of the biomarker in a portion of cells which appears to benon-cancerous, and then comparing this normal level of expression withthe level of expression in a portion of the tumor cells. Alternately,and particularly as further information becomes available as a result ofroutine performance of the methods described herein, population-averagevalues for normal expression of the biomarkers of the invention may beused. In other embodiments, the ‘normal’ level of expression of abiomarker may be determined by assessing expression of the biomarker ina patient sample obtained from a non-cancer-afflicted patient, from apatient sample obtained from a patient before the suspected onset ofcancer in the patient, from archived patient samples, and the like.

An exemplary method for detecting the presence or absence of a biomarkerprotein or nucleic acid in a biological sample involves obtaining abiological sample (e.g. a tumor-associated body fluid) from a testsubject and contacting the biological sample with a compound or an agentcapable of detecting the polypeptide or nucleic acid (e.g., MRNA,genomic DNA, or cDNA). The detection methods of the invention can thusbe used to detect mRNA, protein, cDNA, or genomic DNA, for example, in abiological sample in vitro as well as in vivo. For example, in vitrotechniques for detection of MRNA include Northern hybridizations and insitu hybridizations. In vitro techniques for detection of a biomarkerprotein include enzyme linked immunosorbent assays (ELISAs), Westernblots, immunoprecipitations and immunofluorescence. In vitro techniquesfor detection of genomic DNA include Southern hybridizations. In vivotechniques for detection of mRNA include polymerase chain reaction(PCR), Northern hybridizations and in situ hybridizations. Furthermore,in vivo techniques for detection of a biomarker protein includeintroducing into a subject a labeled antibody directed against theprotein or fragment thereof. For example, the antibody can be labeledwith a radioactive marker whose presence and location in a subject canbe detected by standard imaging techniques.

A general principle of such diagnostic and prognostic assays involvespreparing a sample or reaction mixture that may contain a biomarker, anda probe, under appropriate conditions and for a time sufficient to allowthe biomarker and probe to interact and bind, thus forming a complexthat can be removed and/or detected in the reaction mixture. Theseassays can be conducted in a variety of ways.

For example, one method to conduct such an assay would involve anchoringthe biomarker or probe onto a solid phase support, also referred to as asubstrate, and detecting target biomarker/probe complexes anchored onthe solid phase at the end of the reaction. In one embodiment of such amethod, a sample from a subject, which is to be assayed for presenceand/or concentration of biomarker, can be anchored onto a carrier orsolid phase support. In another embodiment, the reverse situation ispossible, in which the probe can be anchored to a solid phase and asample from a subject can be allowed to react as an unanchored componentof the assay.

There are many established methods for anchoring assay components to asolid phase. These include, without limitation, biomarker or probemolecules which are immobilized through conjugation of biotin andstreptavidin. Such biotinylated assay components can be prepared frombiotin-NHS (N-hydroxy-succinimide) using techniques known in the art(e.g., biotinylation kit, Pierce Chemicals, Rockford, Ill.), andimmobilized in the wells of streptavidin-coated 96 well plates (PierceChemical). In certain embodiments, the surfaces with immobilized assaycomponents can be prepared in advance and stored.

Other suitable carriers or solid phase supports for such assays includeany material capable of binding the class of molecule to which thebiomarker or probe belongs. Well-known supports or carriers include, butare not limited to, glass, polystyrene, nylon, polypropylene, nylon,polyethylene, dextran, amylases, natural and modified celluloses,polyacrylamides, gabbros, and magnetite.

In order to conduct assays with the above mentioned approaches, thenon-immobilized component is added to the solid phase upon which thesecond component is anchored. After the reaction is complete,uncomplexed components may be removed (e.g., by washing) underconditions such that any complexes formed will remain immobilized uponthe solid phase. The detection of biomarker/probe complexes anchored tothe solid phase can be accomplished in a number of methods outlinedherein.

In one embodiment, the probe, when it is the unanchored assay component,can be labeled for the purpose of detection and readout of the assay,either directly or indirectly, with detectable labels discussed hereinand which are well-known to one skilled in the art.

It is also possible to directly detect biomarker/probe complex formationwithout further manipulation or labeling of either component (biomarkeror probe), for example by utilizing the technique of fluorescence energytransfer (i.e. FET, see for example, Lakowicz et al., U.S. Pat. No.5,631,169; Stavrianopoulos, et al., U.S. Pat. No. 4,868,103). Afluorophore label on the first, ‘donor’ molecule is selected such that,upon excitation with incident light of appropriate wavelength, itsemitted fluorescent energy will be absorbed by a fluorescent label on asecond ‘acceptor’ molecule, which in turn is able to fluoresce due tothe absorbed energy. Alternately, the ‘donor’ protein molecule maysimply utilize the natural fluorescent energy of tryptophan residues.Labels are chosen that emit different wavelengths of light, such thatthe ‘acceptor’ molecule label may be differentiated from that of the‘donor’. Since the efficiency of energy transfer between the labels isrelated to the distance separating the molecules, spatial relationshipsbetween the molecules can be assessed. In a situation in which bindingoccurs between the molecules, the fluorescent emission of the ‘acceptor’molecule label in the assay should be maximal. An FET binding event canbe conveniently measured through standard fluorometric detection meanswell known in the art (e.g., using a fluorimeter).

In another embodiment, determination of the ability of a probe torecognize a biomarker can be accomplished without labeling either assaycomponent (probe or biomarker) by utilizing a technology such asreal-time Biomolecular Interaction Analysis (BIA) (see, e.g., Sjolander,S. and Urbaniczky, C., 1991, Anal. Chem. 63:2338-2345 and Szabo et al.,1995, Curr. Opin. Struct. Biol. 5:699-705). As used herein, “BIA” or“surface plasmon resonance” is a technology for studying biospecificinteractions in real time, without labeling any of the interactants(e.g., BIAcore). Changes in the mass at the binding surface (indicativeof a binding event) result in alterations of the refractive index oflight near the surface (the optical phenomenon of surface plasmonresonance (SPR)), resulting in a detectable signal which can be used asan indication of real-time reactions between biological molecules.

Alternatively, in another embodiment, analogous diagnostic andprognostic assays can be conducted with biomarker and probe as solutesin a liquid phase. In such an assay, the complexed biomarker and probeare separated from uncomplexed components by any of a number of standardtechniques, including but not limited to: differential centrifugation,chromatography, electrophoresis and immunoprecipitation. In differentialcentrifugation, biomarker/probe complexes may be separated fromuncomplexed assay components through a series of centrifugal steps, dueto the different sedimentation equilibria of complexes based on theirdifferent sizes and densities (see, for example, Rivas, G., and Minton,A. P., 1993, Trends Biochem Sci. 18(8):284-7). Standard chromatographictechniques may also be utilized to separate complexed molecules fromuncomplexed ones. For example, gel filtration chromatography separatesmolecules based on size, and through the utilization of an appropriategel filtration resin in a column format, for example, the relativelylarger complex may be separated from the relatively smaller uncomplexedcomponents. Similarly, the relatively different charge properties of thebiomarker/probe complex as compared to the uncomplexed components may beexploited to differentiate the complex from uncomplexed components, forexample through the utilization of ion-exchange chromatography resins.Such resins and chromatographic techniques are well known to one skilledin the art (see, e.g., Heegaard, N. H., 1998, J. Mol. Recognit. Winter11(1-6):141-8; Hage, D. S., and Tweed, S. A. J. Chromatogr B Biomed SciAppl 1997 Oct. 10;699(1-2):499-525). Gel electrophoresis may also beemployed to separate complexed assay components from unbound components(see, e.g., Ausubel et al., ed., Current Protocols in Molecular Biology,John Wiley & Sons, New York, 1987-1999). In this technique, protein ornucleic acid complexes are separated based on size or charge, forexample. In order to maintain the binding interaction during theelectrophoretic process, non-denaturing gel matrix materials andconditions in the absence of reducing agent are typically preferred.Appropriate conditions to the particular assay and components thereofwill be well known to one skilled in the art.

In a particular embodiment, the level of biomarker mRNA can bedetermined both by in situ and by in vitro formats in a biologicalsample using methods known in the art. The term “biological sample” isintended to include tissues, cells, biological fluids and isolatesthereof, isolated from a subject, as well as tissues, cells and fluidspresent within a subject. Many expression detection methods use isolatedRNA. For in vitro methods, any RNA isolation technique that does notselect against the isolation of mRNA can be utilized for thepurification of RNA from tumor cells (see, e.g., Ausubel et al., ed.,Current Protocols in Molecular Biology, John Wiley & Sons, New York1987-1999). Additionally, large numbers of tissue samples can readily beprocessed using techniques well known to those of skill in the art, suchas, for example, the single-step RNA isolation process of Chomczynski(1989, U.S. Pat. No. 4,843,155).

The isolated MRNA can be used in hybridization or amplification assaysthat include, but are not limited to, Southern or Northern analyses,polymerase chain reaction analyses and probe arrays. One preferreddiagnostic method for the detection of MRNA levels involves contactingthe isolated MRNA with a nucleic acid molecule (probe) that canhybridize to the MRNA encoded by the gene being detected. The nucleicacid probe can be, for example, a full-length cDNA, or a portionthereof, such as an oligonucleotide of at least 7, 15, 30, 50, 100, 250or 500 nucleotides in length and sufficient to specifically hybridizeunder stringent conditions to a MRNA or genomic DNA encoding a biomarkerof the present invention. Other suitable probes for use in thediagnostic assays of the invention are described herein. Hybridizationof an MRNA with the probe indicates that the biomarker in question isbeing expressed.

In one format, the mRNA is immobilized on a solid surface and contactedwith a probe, for example by running the isolated MRNA on an agarose geland transferring the MRNA from the gel to a membrane, such asnitrocellulose. In an alternative format, the probe(s) are immobilizedon a solid surface and the mRNA is contacted with the probe(s), forexample, in an Affymetrix gene chip array. A skilled artisan can readilyadapt known mRNA detection methods for use in detecting the level ofMRNA encoded by the biomarkers of the present invention.

An alternative method for determining the level of mRNA biomarker in asample involves the process of nucleic acid amplification, e.g., byRT-PCR (the experimental embodiment set forth in Mullis, 1987, U.S. Pat.No. 4,683,202), ligase chain reaction (Barany, 1991, Proc. Natl. Acad.Sci. USA, 88:189-193), self sustained sequence replication (Guatelli etal., 1990, Proc. Natl. Acad. Sci. USA 87:1874-1878), transcriptionalamplification system (Kwoh et al., 1989, Proc. Natl. Acad. Sci. USA86:1173-1177), Q-Beta Replicase (Lizardi et al., 1988, Bio/Technology6:1197), rolling circle replication (Lizardi et al., U.S. Pat. No.5,854,033) or any other nucleic acid amplification method, followed bythe detection of the amplified molecules using techniques well known tothose of skill in the art. These detection schemes are especially usefulfor the detection of nucleic acid molecules if such molecules arepresent in very low numbers. As used herein, amplification primers aredefined as being a pair of nucleic acid molecules that can anneal to 5′or 3′ regions of a gene (plus and minus strands, respectively, orvice-versa) and contain a short region in between. In general,amplification primers are from about 10 to 30 nucleotides in length andflank a region from about 50 to 200 nucleotides in length. Underappropriate conditions and with appropriate reagents, such primerspermit the amplification of a nucleic acid molecule comprising thenucleotide sequence flanked by the primers.

For in situ methods, mRNA does not need to be isolated from the tumorcells prior to detection. In such methods, a cell or tissue sample isprepared/processed using known histological methods. The sample is thenimmobilized on a support, typically a glass slide, and then contactedwith a probe that can hybridize to mRNA that encodes the biomarker.

As an alternative to making determinations based on the absoluteexpression level of the biomarker, determinations may be based on thenormalized expression level of the biomarker. Expression levels arenormalized by correcting the absolute expression level of a biomarker bycomparing its expression to the expression of a gene that is not abiomarker, e.g., a housekeeping gene that is constitutively expressed.Suitable genes for normalization include housekeeping genes such as theactin gene, or epithelial cell-specific genes. This normalization allowsthe comparison of the expression level in one sample, e.g., a patientsample, to another sample, e.g., a non-tumor sample, or between samplesfrom different sources.

Alternatively, the expression level can be provided as a relativeexpression level. To determine a relative expression level of abiomarker (e.g. a mesenchymal biomarker), the level of expression of thebiomarker is determined for 10 or more samples of normal versus cancercell isolates, preferably 50 or more samples, prior to the determinationof the expression level for the sample in question. The mean expressionlevel of each of the genes assayed in the larger number of samples isdetermined and this is used as a baseline expression level for thebiomarker. The expression level of the biomarker determined for the testsample (absolute level of expression) is then divided by the meanexpression value obtained for that biomarker. This provides a relativeexpression level.

In another embodiment of the present invention, a biomarker protein isdetected. A preferred agent for detecting biomarker protein of theinvention is an antibody capable of binding to such a protein or afragment thereof, preferably an antibody with a detectable label.Antibodies can be polyclonal, or more preferably, monoclonal. An intactantibody, or a fragment or derivative thereof (e.g., Fab orF(ab′).sub.2) can be used. The term “labeled”, with regard to the probeor antibody, is intended to encompass direct labeling of the probe orantibody by coupling (i.e., physically linking) a detectable substanceto the probe or antibody, as well as indirect labeling of the probe orantibody by reactivity with another reagent that is directly labeled.Examples of indirect labeling include detection of a primary antibodyusing a fluorescently labeled secondary antibody and end-labeling of aDNA probe with biotin such that it can be detected with fluorescentlylabeled streptavidin.

Proteins from tumor cells can be isolated using techniques that are wellknown to those of skill in the art. The protein isolation methodsemployed can, for example, be such as those described in Harlow and Lane(Harlow and Lane, 1988, Antibodies: A Laboratory Manual, Cold SpringHarbor Laboratory Press, Cold Spring Harbor, N.Y.).

A variety of formats can be employed to determine whether a samplecontains a protein that binds to a given antibody. Examples of suchformats include, but are not limited to, enzyme immunoassay (EIA),radioimmunoassay (RIA), Western blot analysis and enzyme linkedimmunoabsorbant assay (ELISA). A skilled artisan can readily adapt knownprotein/antibody detection methods for use in determining whether tumorcells express a biomarker of the present invention.

In one format, antibodies, or antibody fragments or derivatives, can beused in methods such as Western blots or immunofluorescence techniquesto detect the expressed proteins. In such uses, it is generallypreferable to immobilize either the antibody or proteins on a solidsupport. Suitable solid phase supports or carriers include any supportcapable of binding an antigen or an antibody. Well-known supports orcarriers include glass, polystyrene, polypropylene, polyethylene,dextran, nylon, amylases, natural and modified celluloses,polyacrylamides, gabbros, and magnetite.

One skilled in the art will know many other suitable carriers forbinding antibody or antigen, and will be able to adapt such support foruse with the present invention. For example, protein isolated from tumorcells can be run on a polyacrylamide gel electrophoresis and immobilizedonto a solid phase support such as nitrocellulose. The support can thenbe washed with suitable buffers followed by treatment with thedetectably labeled antibody. The solid phase support can then be washedwith the buffer a second time to remove unbound antibody. The amount ofbound label on the solid support can then be detected by conventionalmeans.

For ELISA assays, specific binding pairs can be of the immune ornon-immune type. Immune specific binding pairs are exemplified byantigen-antibody systems or hapten/anti-hapten systems. There can bementioned fluorescein/anti-fluorescein,dinitrophenyl/anti-dinitrophenyl, biotin/anti-biotin,peptide/anti-peptide and the like. The antibody member of the specificbinding pair can be produced by customary methods familiar to thoseskilled in the art. Such methods involve immunizing an animal with theantigen member of the specific binding pair. If the antigen member ofthe specific binding pair is not immunogenic, e.g., a hapten, it can becovalently coupled to a carrier protein to render it immunogenic.Non-immune binding pairs include systems wherein the two componentsshare a natural affinity for each other but are not antibodies.Exemplary non-immune pairs are biotin-streptavidin, intrinsicfactor-vitamin B₁₂, folic acid-folate binding protein and the like.

A variety of methods are available to covalently label antibodies withmembers of specific binding pairs. Methods are selected based upon thenature of the member of the specific binding pair, the type of linkagedesired, and the tolerance of the antibody to various conjugationchemistries. Biotin can be covalently coupled to antibodies by utilizingcommercially available active derivatives. Some of these arebiotin-N-hydroxy-succinimide which binds to amine groups on proteins;biotin hydrazide which binds to carbohydrate moieties, aldehydes andcarboxyl groups via a carbodiimide coupling; and biotin maleimide andiodoacetyl biotin which bind to sulfhydryl groups. Fluorescein can becoupled to protein amine groups using fluorescein isothiocyanate.Dinitrophenyl groups can be coupled to protein amine groups using2,4-dinitrobenzene sulfate or 2,4-dinitrofluorobenzene. Other standardmethods of conjugation can be employed to couple monoclonal antibodiesto a member of a specific binding pair including dialdehyde,carbodiimide coupling, homofunctional crosslinking, andheterobifunctional crosslinking. Carbodiimide coupling is an effectivemethod of coupling carboxyl groups on one substance to amine groups onanother. Carbodiimide coupling is facilitated by using the commerciallyavailable reagent 1-ethyl-3-(dimethyl-aminopropyl)-carbodiimide (EDAC).

Homobifunctional crosslinkers, including the bifunctional imidoestersand bifunctional N-hydroxysuccinimide esters, are commercially availableand are employed for coupling amine groups on one substance to aminegroups on another. Heterobifunctional crosslinkers are reagents whichpossess different functional groups. The most common commerciallyavailable heterobifunctional crosslinkers have an amine reactiveN-hydroxysuccinimide ester as one functional group, and a sulfhydrylreactive group as the second functional group. The most commonsulfhydryl reactive groups are maleimides, pyridyl disulfides and activehalogens. One of the functional groups can be a photoactive arylnitrene, which upon irradiation reacts with a variety of groups.

The detectably-labeled antibody or detectably-labeled member of thespecific binding pair is prepared by coupling to a reporter, which canbe a radioactive isotope, enzyme, fluorogenic, chemiluminescent orelectrochemical materials. Two commonly used radioactive isotopes are¹²⁵I and ³H. Standard radioactive isotopic labeling procedures includethe chloramine T, lactoperoxidase and Bolton-Hunter methods for ¹²⁵I andreductive methylation for ³H. The term “detectably-labeled” refers to amolecule labeled in such a way that it can be readily detected by theintrinsic enzymic activity of the label or by the binding to the labelof another component, which can itself be readily detected.

Enzymes suitable for use in this invention include, but are not limitedto, horseradish peroxidase, alkaline phosphatase, β-galactosidase,glucose oxidase, luciferases, including firefly and renilla,β-lactamase, urease, green fluorescent protein (GFP) and lysozyme.Enzyme labeling is facilitated by using dialdehyde, carbodiimidecoupling, homobifunctional crosslinkers and heterobifunctionalcrosslinkers as described above for coupling an antibody with a memberof a specific binding pair.

The labeling method chosen depends on the functional groups available onthe enzyme and the material to be labeled, and the tolerance of both tothe conjugation conditions. The labeling method used in the presentinvention can be one of, but not limited to, any conventional methodscurrently employed including those described by Engvall and Pearlmann,Immunochemistry 8, 871 (1971), Avrameas and Ternynck, Immunochemistry 8,1175 (1975), Ishikawa et al., J. Immunoassay 4(3):209-327 (1983) andJablonski, Anal. Biochem. 148:199 (1985).

Labeling can be accomplished by indirect methods such as using spacersor other members of specific binding pairs. An example of this is thedetection of a biotinylated antibody with unlabeled streptavidin andbiotinylated enzyme, with streptavidin and biotinylated enzyme beingadded either sequentially or simultaneously. Thus, according to thepresent invention, the antibody used to detect can be detectably-labeleddirectly with a reporter or indirectly with a first member of a specificbinding pair. When the antibody is coupled to a first member of aspecific binding pair, then detection is effected by reacting theantibody-first member of a specific binding complex with the secondmember of the binding pair that is labeled or unlabeled as mentionedabove.

Moreover, the unlabeled detector antibody can be detected by reactingthe unlabeled antibody with a labeled antibody specific for theunlabeled antibody. In this instance “detectably-labeled” as used aboveis taken to mean containing an epitope by which an antibody specific forthe unlabeled antibody can bind. Such an anti-antibody can be labeleddirectly or indirectly using any of the approaches discussed above. Forexample, the anti-antibody can be coupled to biotin which is detected byreacting with the streptavidin-horseradish peroxidase system discussedabove.

In one embodiment of this invention biotin is utilized. The biotinylatedantibody is in turn reacted with streptavidin-horseradish peroxidasecomplex. Orthophenylenediamine, 4-chloro-naphthol, tetramethylbenzidine(TMB), ABTS, BTS or ASA can be used to effect chromogenic detection.

In one immunoassay format for practicing this invention, a forwardsandwich assay is used in which the capture reagent has beenimmobilized, using conventional techniques, on the surface of a support.Suitable supports used in assays include synthetic polymer supports,such as polypropylene, polystyrene, substituted polystyrene, e.g.aminated or carboxylated polystyrene, polyacrylamides, polyamides,polyvinylchloride, glass beads, agarose, or nitrocellulose.

The invention also encompasses kits for detecting the presence of abiomarker protein or nucleic acid in a biological sample. Such kits canbe used to determine if a subject is suffering from or is at increasedrisk of developing a tumor that is less susceptible to inhibition byEGFR kinase inhibitors. For example, the kit can comprise a labeledcompound or agent capable of detecting a biomarker protein or nucleicacid in a biological sample and means for determining the amount of theprotein or mRNA in the sample (e.g., an antibody which binds the proteinor a fragment thereof, or an oligonucleotide probe which binds to DNA orMRNA encoding the protein). Kits can also include instructions forinterpreting the results obtained using the kit.

For antibody-based kits, the kit can comprise, for example: (1) a firstantibody (e.g., attached to a solid support) which binds to a biomarkerprotein; and, optionally, (2) a second, different antibody which bindsto either the protein or the first antibody and is conjugated to adetectable label.

For oligonucleotide-based kits, the kit can comprise, for example: (1)an oligonucleotide, e.g., a detectably labeled oligonucleotide, whichhybridizes to a nucleic acid sequence encoding a biomarker protein or(2) a pair of primers useful for amplifying a biomarker nucleic acidmolecule. The kit can also comprise, e.g., a buffering agent, apreservative, or a protein stabilizing agent. The kit can furthercomprise components necessary for detecting the detectable label (e.g.,an enzyme or a substrate). The kit can also contain a control sample ora series of control samples which can be assayed and compared to thetest sample. Each component of the kit can be enclosed within anindividual container and all of the various containers can be within asingle package, along with instructions for interpreting the results ofthe assays performed using the kit.

The present invention further provides a method for treating tumors ortumor metastases in a patient, comprising the steps of diagnosing apatient's likely responsiveness to an EGFR kinase inhibitor by assessingwhether the tumor cells have undergone an epithelial-mesenchymaltransition, by for example any of the methods described herein fordetermining the expression level of tumor cell epithelial and/ormesenchymal biomarkers, and administering to said patient atherapeutically effective amount of an EGFR kinase inhibitor. For thismethod, an example of a preferred EGFR kinase inhibitor would beerlotinib, including pharmacologically acceptable salts or polymorphsthereof. In this method one or more additional anti-cancer agents ortreatments can be co-administered simultaneously or sequentially withthe EGFR kinase inhibitor, as judged to be appropriate by theadministering physician given the prediction of the likelyresponsiveness of the patient to an EGFR kinase inhibitor, incombination with any additional circumstances pertaining to theindividual patient.

It will be appreciated by one of skill in the medical arts that theexact manner of administering to said patient of a therapeuticallyeffective amount of an EGFR kinase inhibitor following a diagnosis of apatient's likely responsiveness to an EGFR kinase inhibitor will be atthe discretion of the attending physician. The mode of administration,including dosage, combination with other anti-cancer agents, timing andfrequency of administration, and the like, may be affected by thediagnosis of a patient's likely responsiveness to an EGFR kinaseinhibitor, as well as the patient's condition and history. Thus, evenpatients diagnosed with tumors predicted to be relatively insensitive toEGFR kinase inhibitors may still benefit from treatment with suchinhibitors, particularly in combination with other anti-cancer agents,or agents that may alter a tumor's sensitivity to EGFR kinaseinhibitors.

The present invention further provides a method for treating tumors ortumor metastases in a patient, comprising the steps of diagnosing apatient's likely responsiveness to an EGFR kinase inhibitor by assessingwhether the tumor cells have undergone an epithelial-mesenchymaltransition, by for example any of the methods described herein fordetermining the expression level of tumor cell epithelial and/ormesenchymal biomarkers, identifying the patient as one who is likely todemonstrate an effective response to treatment with an EGFR kinaseinhibitor, and administering to said patient a therapeutically effectiveamount of an EGFR kinase inhibitor.

The present invention further provides a method for treating tumors ortumor metastases in a patient, comprising the steps of diagnosing apatient's likely responsiveness to an EGFR kinase inhibitor by assessingwhether the tumor cells have undergone an epithelial-mesenchymaltransition, by for example any of the methods described herein fordetermining the expression level of tumor cell epithelial and/ormesenchymal biomarkers, identifying the patient as one who is lesslikely or not likely to demonstrate an effective response to treatmentwith an EGFR kinase inhibitor, and treating said patient with ananti-cancer therapy other than an EGFR kinase inhibitor.

The present invention further provides a method of identifying anepithelial biomarker whose expression level is predictive of thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, comprising: (a) measuring the expression level of a candidateepithelial biomarker in a panel of tumor cells that displays a range ofsensitivities to an EGFR kinase inhibitor, and (b) identifying acorrelation between the expression level of said candidate epithelialbiomarker in the tumor cells and the sensitivity of tumor cell growth toinhibition by the EGFR kinase inhibitor, wherein a correlation of highlevels of the epithelial biomarker with high sensitivity of tumor cellgrowth to inhibition by the EGFR kinase inhibitor indicates that theexpression level of said epithelial biomarker is predictive of thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor. In one embodiment of this method the panel of tumor cells isa panel of tumor cell lines. In an alternative embodiment the panel oftumor cells is a panel of primary tumor cells, prepared from tumorsamples derived from patients or experimental animal models. In anadditional embodiment the panel of tumor cells is a panel of tumor celllines in mouse xenografts, wherein tumor cell growth can for example bedetermined by monitoring a molecular marker of growth or a grossmeasurement of tumor growth, e.g. tumor dimensions or weight.

The present invention further provides a method of identifying amesenchymal biomarker whose expression level is predictive of thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, comprising: (a) measuring the expression level of a candidatemesenchymal biomarker in a panel of tumor cells that displays a range ofsensitivities to an EGFR kinase inhibitor, and (b) identifying acorrelation between the expression level of said candidate mesenchymalbiomarker in the tumor cells and the sensitivity of tumor cell growth toinhibition by the EGFR kinase inhibitor, wherein a correlation of highlevels of the mesenchymal biomarker with low sensitivity of tumor cellgrowth to inhibition by the EGFR kinase inhibitor indicates that theexpression level of said mesenchymal biomarker is predictive of the lackof sensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor. In one embodiment of this method the panel of tumor cells isa panel of tumor cell lines. In an alternative embodiment the panel oftumor cells is a panel of primary tumor cells, prepared from tumorsamples derived from patients or experimental animal models. In anadditional embodiment the panel of tumor cells is a panel of tumor celllines in mouse xenografts, wherein tumor cell growth can for example bedetermined by monitoring a molecular marker of growth or a grossmeasurement of tumor growth, e.g. tumor dimensions or weight.

The present invention further provides a method of identifying anepithelial biomarker that is diagnostic for more effective treatment ofa neoplastic condition with an EGFR kinase inhibitor, comprising: (a)measuring the level of a candidate epithelial biomarker in neoplasticcell-containing samples from patients with a neoplastic condition, and(b) identifying a correlation between the level of said candidateepithelial biomarker in the sample from the patient with theeffectiveness of treatment of the neoplastic condition with an EGFRkinase inhibitor, wherein a correlation of high levels of the epithelialbiomarker with more effective treatment of the neoplastic condition withan EGFR kinase inhibitor indicates that said epithelial biomarker isdiagnostic for more effective treatment of the neoplastic condition withan EGFR kinase inhibitor.

The present invention further provides a method of identifying amesenchymal biomarker that is diagnostic for less effective treatment ofa neoplastic condition with an EGFR kinase inhibitor, comprising: (a)measuring the level of a candidate mesenchymal biomarker in neoplasticcell-containing samples from patients with a neoplastic condition, and(b) identifying a correlation between the level of said candidatemesenchymal biomarker in the sample from the patient with theeffectiveness of treatment of the neoplastic condition with an EGFRkinase inhibitor, wherein a correlation of high levels of themesenchymal biomarker with less effective treatment of the neoplasticcondition with an EGFR kinase inhibitor indicates that said mesenchymalbiomarker is diagnostic for less effective treatment of the neoplasticcondition with an EGFR kinase inhibitor.

The effectiveness of treatment in the preceding methods can for examplebe determined by measuring the decrease in size of tumors present in thepatients with the neoplastic condition, or by assaying a moleculardeterminant of the degree of proliferation of the tumor cells.

The present invention provides a method of identifying an epithelialbiomarker that is diagnostic for increased survival of a patient with aneoplastic condition when treated with an EGFR kinase inhibitor,comprising: (a) measuring the level of the candidate epithelialbiomarker in neoplastic cell-containing samples from patients with aneoplastic condition, and (b) identifying a correlation between thelevel of said candidate epithelial biomarker in the sample from thepatient with the survival of that patient when treated with an EGFRkinase inhibitor, wherein the correlation of an epithelial biomarkerwith survival in said patients indicates said epithelial biomarker isdiagnostic for increased survival of a patient with said neoplasticcondition when treated with an EGFR kinase inhibitor.

The present invention provides a method of identifying a mesenchymalbiomarker that is diagnostic for decreased survival of a patient with aneoplastic condition when treated with an EGFR kinase inhibitor,comprising: (a) measuring the level of the candidate mesenchymalbiomarker in neoplastic cell-containing samples from patients with aneoplastic condition, and (b) identifying an inverse correlation betweenthe level of said candidate mesenchymal biomarker in the sample from thepatient with the survival of that patient when treated with an EGFRkinase inhibitor, wherein the inverse correlation of a mesenchymalbiomarker with survival in said patients indicates said mesenchymalbiomarker is diagnostic for decreased survival of a patient with saidneoplastic condition when treated with an EGFR kinase inhibitor.

The present invention provides a method for the identification of anagent that enhances sensitivity of the growth of a tumor cell to an EGFRkinase inhibitor, said tumor cell having being characterized as one thathas previously undergone an epithelial-mesenchymal transition,comprising contacting a sample of said tumor cells with an EGFR kinaseinhibitor, contacting an identical sample of said tumor cells with anEGFR kinase inhibitor in the presence of a test agent, comparing theEGFR kinase inhibitor-mediated growth inhibition in the presence andabsence of the test agent, and determining whether the test agent is anagent that enhances sensitivity of the growth of the tumor cell to anEGFR kinase inhibitor. For this method, an example of a preferred EGFRkinase inhibitor would be erlotinib, including pharmacologicallyacceptable salts or polymorphs thereof. In one embodiment of this methodthe sample of tumor cells can be cells in vitro, such as a tumor cellline or a primary tumor cell culture. In an alternative embodiment thesample of tumor cells can be cells in vivo, such as tumor cells in amouse xenograft. In the latter embodiment, tumor cell growth can forexample be determined by monitoring a molecular marker of growth or agross measurement of tumor growth, e.g. tumor dimensions or weight.

Suitable test agents which can be tested in the preceding method includecombinatorial libraries, defined chemical entities, peptide and peptidemimetics, oligonucleotides and natural product libraries, such asdisplay (e.g. phage display libraries) and antibody products. Testagents may be used in an initial screen of, for example, 10 substancesper reaction, and the substances of these batches which show inhibitionor activation tested individually. Test agents may be used at aconcentration of from 1 nM to 1000 μM, preferably from 1 μM to 100 μM,more preferably from 1 μM to 10 μM.

Agents which enhances sensitivity of the growth of a tumor cell to anEGFR kinase inhibitor which have been identified by the precedingmethods can be used in the treatment of patients with cancers which arepredicted to be less responsive to inhibition by EGFR kinase inhibitors(including lung cancer, pancreatic cancer, or any of the other cancertypes described herein), and are an additional embodiment of thisinvention. Thus the present invention further provides a composition ofmatter comprising such an agent, which may be formulated andadministered by any of the methods known in the art, including thosedescribed herein in relation to EGFR kinase inhibitors. Such agents thatenhances sensitivity of the growth of a tumor cell to an EGFR kinaseinhibitor may for example be agents that induce a mesenchymal toepithelial transition (MET), or that inhibit a specific cellularactivity responsible for reduced sensitivity to EGFR kinase inhibitors,or induce a specific cellular activity that enhances sensitivity to EGFRkinase inhibitors. Examples of suitable agents include antagonists ofEMT inducing agents, TGF-beta antagonists or TGF-beta receptorantagonists (for example: anti-TGF-beta and anti-TGF-beta receptorantibodies,4-(4-Fluorophenyl)-2-(4-methylsulfinylphenyl)-5-(4-pyridyl)-1H-imidazole(SB 203580);4-[4-(3,4-Methylenedioxyphenyl)-5-(2-pyridyl)-1H-imidazol-2-yl]-benzamide(SB431542); and similarly or more active analogues or homologues of suchcompounds), inhibitors of FAK, ILK, SRC, FYN or YES protein-tyrosinekinases, and calpain inhibitors.

The present invention further provides a method of treating tumors ortumor metastases in a patient, comprising administering to the patient atherapetucially effective amount of an EGFR kinase inhibitor and inaddition, simultaneously or sequentially, one or more antagonists of anEMT inducing agent. In a preferred embodiment said tumor is firstdetermined to have epithelial phenotype by the presence one or moreepithelial biomarkers. In a particular embodiment, said EMT inducingagent is an anti-TGF-beta antibody, an anti-TGF-beta receptor antibody,4-(4-Fluorophenyl)-2-(4-methylsulfinylphenyl)-5-(4-pyridyl)-1H-imidazole(SB 203580); or4-[4-(3,4-Methylenedioxyphenyl)-5-(2-pyridyl)-1H-imidazol-2-yl]-benzamide(SB431542). In a particular embodiment, said EGFR antagonist iserlotinib.

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously or sequentially,one or more other cytotoxic, chemotherapeutic or anti-cancer agents, orcompounds that enhance the effects of such agents.

In the context of this invention, additional other cytotoxic,chemotherapeutic or anti-cancer agents, or compounds that enhance theeffects of such agents, include, for example: alkylating agents oragents with an alkylating action, such as cyclophosphamide (CTX; e.g.CYTOXAN®), chlorambucil (CHL; e.g. LEUKERAN®), cisplatin (CisP; e.g.PLATINOL®) busulfan (e.g. MYLERAN®), melphalan, carmustine (BCNU),streptozotocin, triethylenemelamine (TEM), mitomycin C, and the like;anti-metabolites, such as methotrexate (MTX), etoposide (VP16; e.g.VEPESID®), 6-mercaptopurine (6MP), 6-thiocguanine (6TG), cytarabine(Ara-C), 5-fluorouracil (5-FU), capecitabine (e.g.XELODA®), dacarbazine(DTIC), and the like; antibiotics, such as actinomycin D, doxorubicin(DXR; e.g. ADRIAMYCIN®), daunorubicin (daunomycin), bleomycin,mithramycin and the like; alkaloids, such as vinca alkaloids such asvincristine (VCR), vinblastine, and the like; and other antitumoragents, such as paclitaxel (e.g. TAXOL®) and pactitaxel derivatives, thecytostatic agents, glucocorticoids such as dexamethasone (DEX; e.g.DECADRON®) and corticosteroids such as prednisone, nucleoside enzymeinhibitors such as hydroxyurea, amino acid depleting enzymes such asasparaginase, leucovorin and other folic acid derivatives, and similar,diverse antitumor agents. The following agents may also be used asadditional agents: arnifostine (e.g. ETHYOL®), dactinomycin,mechlorethamine (nitrogen mustard), streptozocin, cyclophosphamide,lomustine (CCNU), doxorubicin lipo (e.g. DOXIL®), gemcitabine (e.g.GEMZAR®), daunorubicin lipo (e.g. DAUNOXOME®), procarbazine, mitomycin,docetaxel (e.g. TAXOTERE®), aldesleukin, carboplatin, oxaliplatin,cladribine, camptothecin, CPT 11 (irinotecan), 10-hydroxy7-ethyl-camptothecin (SN38), floxuridine, fludarabine, ifosfamide,idarubicin, mesna, interferon beta, interferon alpha, mitoxantrone,topotecan, leuprolide, megestrol, melphalan, mercaptopurine, plicamycin,mitotane, pegaspargase, pentostatin, pipobroman, plicamycin, tamoxifen,teniposide, testolactone, thioguanine, thiotepa, uracil mustard,vinorelbine, chlorambucil.

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously or sequentially,one or more anti-hormonal agents. As used herein, the term“anti-hormonal agent” includes natural or synthetic organic or peptidiccompounds that act to regulate or inhibit hormone action on tumors.

Antihormonal agents include, for example: steroid receptor antagonists,anti-estrogens such as tamoxifen, raloxifene, aromatase inhibiting4(5)-imidazoles, other aromatase inhibitors, 42-hydroxytamoxifen,trioxifene, keoxifene, LY 117018, onapristone, and toremifene (e.g.FARESTON®); anti-androgens such as flutamide, nilutamide, bicalutamide,leuprolide, and goserelin; and pharmaceutically acceptable salts, acidsor derivatives of any of the above; agonists and/or antagonists ofglycoprotein hormones such as follicle stimulating hormone (FSH),thyroid stimulating hormone (TSH), and luteinizing hormone (LH) and LHRH(leuteinizing hormone-releasing hormone); the LHRH agonist goserelinacetate, commercially available as ZOLADEX® (AstraZeneca); the LHRHantagonist D-alaninamideN-acetyl-3-(2-naphthalenyl)-D-alanyl-4-chloro-D-phenylalanyl-3-(3-pyridinyl)-D-alanyl-L-seryl-N6-(3-pyridinylcarbonyl)-L-lysyl-N6-(3-pyridinylcarbonyl)-D-lysyl-L-leucyl-N6-(1-methylethyl)-L-lysyl-L-proline (e.g ANTIDE®, Ares-Serono); the LHRH antagonist ganirelixacetate; the steroidal anti-androgens cyproterone acetate (CPA) andmegestrol acetate, commercially available as MEGACE® (Bristol-MyersOncology); the nonsteroidal anti-androgen flutamide (2-methyl-N-[4,20-nitro-3-(trifluoromethyl) phenylpropanamide), commercially availableas EULEXIN® (Schering Corp.); the non-steroidal anti-androgennilutamide,(5,5-dimethyl-3-[4-nitro-3-(trifluoromethyl-4′-nitrophenyl)-4,4-dimethyl-imidazolidine-dione);and antagonists for other non-permissive receptors, such as antagonistsfor RAR, RXR, TR, VDR, and the like.

The use of the cytotoxic and other anticancer agents described above inchemotherapeutic regimens is generally well characterized in the cancertherapy arts, and their use herein falls under the same considerationsfor monitoring tolerance and effectiveness and for controllingadministration routes and dosages, with some adjustments. For example,the actual dosages of the cytotoxic agents may vary depending upon thepatient's cultured cell response determined by using histoculturemethods. Generally, the dosage will be reduced compared to the amountused in the absence of additional other agents.

Typical dosages of an effective cytotoxic agent can be in the rangesrecommended by the manufacturer, and where indicated by in vitroresponses or responses in animal models, can be reduced by up to aboutone order of magnitude concentration or amount. Thus, the actual dosagewill depend upon the judgment of the physician, the condition of thepatient, and the effectiveness of the therapeutic method based on the invitro responsiveness of the primary cultured malignant cells orhistocultured tissue sample, or the responses observed in theappropriate animal models.

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously orsequentially,one or more angiogenesis inhibitors.

Anti-angiogenic agents include, for example: VEGFR inhibitors, such asSU-5416 and SU-6668 (Sugen Inc. of South San Francisco, Calif., USA), oras described in, for example International Application Nos. WO 99/24440,WO 99/62890, WO 95/21613, WO 99/61422, WO 98/50356, WO 99/10349, WO97/32856, WO 97/22596, WO 98/54093, WO 98/02438, WO 99/16755, and WO98/02437, and U.S. Pat. Nos. 5,883,113, 5,886,020, 5,792,783, 5,834,504and 6,235,764; VEGF inhibitors such as IM862 (Cytran Inc. of Kirkland,Wash., USA); angiozyme, a synthetic ribozyme from Ribozyme (Boulder,Colo.) and Chiron (Emeryville, Calif.); and antibodies to VEGF, such asbevacizumab (e.g. AVASTIN™, Genentech, South San Francisco, Calif.), arecombinant humanized antibody to VEGF; integrin receptor antagonistsand integrin antagonists, such as to α_(v)β_(3,) α_(v)β₅ and α_(v)β₆integrins, and subtypes thereof, e.g. cilengitide (EMD 121974), or theanti-integrin antibodies, such as for example α_(v)β₃ specific humanizedantibodies (e.g. VITAXIN®); factors such as IFN-alpha (U.S. Pat. Nos.41530,901, 4,503,035, and 5,231,176); angiostatin and plasminogenfragments (e.g. kringle 1-4, kringle 5, kringle 1-3 (O'Reilly, M. S. etal. (1994) Cell 79:315-328; Cao et al. (1996) J. Biol. Chem. 271:29461-29467; Cao et al. (1997) J. Biol. Chem. 272:22924-22928);endostatin (O'Reilly, M. S. et al. (1997) Cell 88:277; and InternationalPatent Publication No. WO 97/15666); thrombospondin (TSP-1; Frazier,(1991) Curr. Opin. Cell Biol. 3:792); platelet factor 4 (PF4);plasminogen activator/urokinase inhibitors; urokinase receptorantagonists; heparinases; fumagillin analogs such as TNP-4701; suraminand suramin analogs; angiostatic steroids; bFGF antagonists; flk-1 andflt-1 antagonists; anti-angiogenesis agents such as MMP-2(matrix-metalloproteinase 2) inhibitors and MMP-9(matrix-metalloproteinase 9) inhibitors. Examples of useful matrixmetalloproteinase inhibitors are described in International PatentPublication Nos. WO 96/33172, WO 96/27583, WO 98/07697, WO 98/03516, WO98/34918, WO 98/34915, WO 98/33768, WO 98/30566, WO 90/05719, WO99/52910, WO 99/52889, WO 99/29667, and WO 99/07675, European PatentPublication Nos. 818,442, 780,386, 1,004,578, 606,046, and 931,788;Great Britain Patent Publication No. 9912961, and U.S. Pat. Nos.5,863,949 and 5,861,510. Preferred MMP-2 and MMP-9 inhibitors are thosethat have little or no activity inhibiting MMP-1. More preferred, arethose that selectively inhibit MMP-2 and/or MMP-9 relative to the othermatrix-metalloproteinases (i.e. MMP-1, MMP-3, MMP-4, MMP-5, MMP-6,MMP-7, MMP-8, MMP-10, MMP-11, MMP-12, and MMP-13).

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously or sequentially,one or more tumor cell pro-apoptotic or apoptosis-stimulating agents.

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously or sequentially,one or more signal transduction inhibitors.

Signal transduction inhibitors include, for example: erbB2 receptorinhibitors, such as organic molecules, or antibodies that bind to theerbB2 receptor, for example, trastuzumab (e.g. HERCEPTIN®); inhibitorsof other protein tyrosine-kinases, e.g. imitinib (e.g. GLEEVEC®); rasinhibitors; raf inhibitors (e.g. BAY 43-9006, Onyx Pharmaceuticals/BayerPharmaceuticals); MEK inhibitors; mTOR inhibitors; cyclin dependentkinase inhibitors; protein kinase C inhibitors; and PDK-1 inhibitors(see Dancey, J. and Sausville, E. A. (2003) Nature Rev. Drug Discovery2:92-313, for a description of several examples of such inhibitors, andtheir use in clinical trials for the treatment of cancer).

ErbB2 receptor inhibitors include, for example: ErbB2 receptorinhibitors, such as GW-282974 (Glaxo Wellcome plc), monoclonalantibodies such as AR-209 (Aronex Pharmaceuticals Inc. of The Woodlands,Tex., USA) and 2B-1 (Chiron), and erbB2 inhibitors such as thosedescribed in International Publication Nos. WO 98/02434, WO 99/35146, WO99/35132, WO 98/02437, WO 97/13760, and WO 95/19970, and U.S. Pat. Nos.5,587,458, 5,877,305, 6,465,449 and 6,541,481.

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously or sequentially,an anti-HER2 antibody or an immunotherapeutically active fragmentthereof.

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously or sequentially,one or more additional anti-proliferative agents.

Additional antiproliferative agents include, for example: Inhibitors ofthe enzyme farnesyl protein transferase and inhibitors of the receptortyrosine kinase PDGFR, including the compounds disclosed and claimed inU.S. Pat. Nos. 6,080,769, 6,194,438, 6,258,824, 6,586,447, 6,071,935,6,495,564, 6,150,377, 6,596,735 and 6,479,513, and International PatentPublication WO 01/40217.

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously or sequentially, aCOX II (cyclooxygenase II ) inhibitor. Examples of useful COX-IIinhibitors include alecoxib (e.g. CELEBREX™), valdecoxib, and rofecoxib.

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously or sequentially,treatment with radiation or a radiopharmaceutical.

The source of radiation can be either external or internal to thepatient being treated. When the source is external to the patient, thetherapy is known as external beam radiation therapy (EBRT). When thesource of radiation is internal to the patient, the treatment is calledbrachytherapy (BT). Radioactive atoms for use in the context of thisinvention can be selected from the group including, but not limited to,radium, cesium-137, iridium-192, americium-241, gold-198, cobalt-57,copper-67, technetium-99, iodine-123, iodine-131, and indium-111. Wherethe EGFR kinase inhibitor according to this invention is an antibody, itis also possible to label the antibody with such radioactive isotopes.

Radiation therapy is a standard treatment for controlling unresectableor inoperable tumors and/or tumor metastases. Improved results have beenseen when radiation therapy has been combined with chemotherapy.Radiation therapy is based on the principle that high-dose radiationdelivered to a target area will result in the death of reproductivecells in both tumor and normal tissues. The radiation dosage regimen isgenerally defined in terms of radiation absorbed dose (Gy), time andfractionation, and must be carefully defined by the oncologist. Theamount of radiation a patient receives will depend on variousconsiderations, but the two most important are the location of the tumorin relation to other critical structures or organs of the body, and theextent to which the tumor has spread. A typical course of treatment fora patient undergoing radiation therapy will be a treatment schedule overa 1 to 6 week period, with a total dose of between 10 and 80 Gyadministered to the patient in a single daily fraction of about 1.8 to2.0 Gy, 5 days a week. In a preferred embodiment of this invention thereis synergy when tumors in human patients are treated with thecombination treatment of the invention and radiation. In other words,the inhibition of tumor growth by means of the agents comprising thecombination of the invention is enhanced when combined with radiation,optionally with additional chemotherapeutic or anticancer agents.Parameters of adjuvant radiation therapies are, for example, containedin International Patent Publication WO 99/60023.

The present invention further provides the preceding methods fortreating tumors or tumor metastases in a patient, comprisingadministering to the patient a therapeutically effective amount of anEGFR kinase inhibitor and in addition, simultaneously or sequentially,treatment with one or more agents capable of enhancing antitumor immuneresponses.

Agents capable of enhancing antitumor immune responses include, forexample: CTLA4 (cytotoxic lymphocyte antigen 4) antibodies (e.g.MDX-CTLA4), and other agents capable of blocking CTLA4. Specific CTLA4antibodies that can be used in the present invention include thosedescribed in U.S. Pat. No. 6,682,736.

In the context of this invention, an “effective amount” of an agent ortherapy is as defined above. A “sub-therapeutic amount” of an agent ortherapy is an amount less than the effective amount for that agent ortherapy, but when combined with an effective or sub-therapeutic amountof another agent or therapy can produce a result desired by thephysician, due to, for example, synergy in the resulting efficaciouseffects, or reduced side effects.

As used herein, the term “patient” preferably refers to a human in needof treatment with an EGFR kinase inhibitor for any purpose, and morepreferably a human in need of such a treatment to treat cancer, or aprecancerous condition or lesion. However, the term “patient” can alsorefer to non-human animals, preferably mammals such as dogs, cats,horses, cows, pigs, sheep and non-human primates, among others, that arein need of treatment with an EGFR kinase inhibitor.

In a preferred embodiment, the patient is a human in need of treatmentfor cancer, a precancerous condition or lesion, or other forms ofabnormal cell growth. The cancer is preferably any cancer treatable,either partially or completely, by administration of an EGFR kinaseinhibitor. The cancer may be, for example, lung cancer, non small celllung (NSCL) cancer, bronchioloalviolar cell lung cancer, bone cancer,pancreatic cancer, skin cancer, cancer of the head or neck, cutaneous orintraocular melanoma, uterine cancer, ovarian cancer, rectal cancer,cancer of the anal region, stomach cancer, gastric cancer, colon cancer,breast cancer, uterine cancer, carcinoma of the fallopian tubes,carcinoma of the endometrium, carcinoma of the cervix, carcinoma of thevagina, carcinoma of the vulva, Hodgkin's Disease, cancer of theesophagus, cancer of the small intestine, cancer of the endocrinesystem, cancer of the thyroid gland, cancer of the parathyroid gland,cancer of the adrenal gland, sarcoma of soft tissue, cancer of theurethra, cancer of the penis, prostate cancer, cancer of the bladder,cancer of the kidney or ureter, renal cell carcinoma, carcinoma of therenal pelvis, mesothelioma, hepatocellular cancer, biliary cancer,chronic or acute leukemia, lymphocytic lymphomas, neoplasms of thecentral nervous system (CNS), spinal axis tumors, brain stem glioma,glioblastoma multiforme, astrocytomas, schwannomas, ependymomas,medulloblastomas, meningiomas, squamous cell carcinomas, pituitaryadenomas, including refractory versions of any of the above cancers, ora combination of one or more of the above cancers. The precancerouscondition or lesion includes, for example, the group consisting of oralleukoplakia, actinic keratosis (solar keratosis), precancerous polyps ofthe colon or rectum, gastric epithelial dysplasia, adenomatousdysplasia, hereditary nonpolyposis colon cancer syndrome (HNPCC),Barrett's esophagus, bladder dysplasia, and precancerous cervicalconditions.

For purposes of the present invention, “co-administration of” and“co-administering” an EGFR kinase inhibitor with an additionalanti-cancer agent (both components referred to hereinafter as the “twoactive agents”) refer to any administration of the two active agents,either separately or together, where the two active agents areadministered as part of an appropriate dose regimen designed to obtainthe benefit of the combination therapy. Thus, the two active agents canbe administered either as part of the same pharmaceutical composition orin separate pharmaceutical compositions. The additional agent can beadministered prior to, at the same time as, or subsequent toadministration of the EGFR kinase inhibitor, or in some combinationthereof. Where the EGFR kinase inhibitor is administered to the patientat repeated intervals, e.g., during a standard course of treatment, theadditional agent can be administered prior to, at the same time as, orsubsequent to, each administration of the EGFR kinase inhibitor, or somecombination thereof, or at different intervals in relation to the EGFRkinase inhibitor treatment, or in a single dose prior to, at any timeduring, or subsequent to the course of treatment with the EGFR kinaseinhibitor.

The EGFR kinase inhibitor will typically be administered to the patientin a dose regimen that provides for the most effective treatment of thecancer (from both efficacy and safety perspectives) for which thepatient is being treated, as known in the art, and as disclosed, e.g. inInternational Patent Publication No. WO 01/34574. In conducting thetreatment method of the present invention, the EGFR kinase inhibitor canbe administered in any effective manner known in the art, such as byoral, topical, intravenous, intra-peritoneal, intramuscular,intra-articular, subcutaneous, intranasal, intra-ocular, vaginal,rectal, or intradermal routes, depending upon the type of cancer beingtreated, the type of EGFR kinase inhibitor being used (for example,small molecule, antibody, RNAi, ribozyme or antisense construct), andthe medical judgement of the prescribing physician as based, e.g., onthe results of published clinical studies.

The amount of EGFR kinase inhibitor administered and the timing of EGFRkinase inhibitor administration will depend on the type (species,gender, age, weight, etc.) and condition of the patient being treated,the severity of the disease or condition being treated, and on the routeof administration. For example, small molecule EGFR kinase inhibitorscan be administered to a patient in doses ranging from 0.001 to 100mg/kg of body weight per day or per week in single or divided doses, orby continuous infusion (see for example, International PatentPublication No. WO 01/34574). In particular, erlotinib HCl can beadministered to a patient in doses ranging from 5-200 mg per day, or100-1600 mg per week, in single or divided doses, or by continuousinfusion. A preferred dose is 150 mg/day. Antibody-based EGFR kinaseinhibitors, or antisense, RNAi or ribozyme constructs, can beadministered to a patient in doses ranging from 0.1 to 100 mg/kg of bodyweight per day or per week in single or divided doses, or by continuousinfusion. In some instances, dosage levels below the lower limit of theaforesaid range may be more than adequate, while in other cases stilllarger doses may be employed without causing any harmful side effect,provided that such larger doses are first divided into several smalldoses for administration throughout the day.

The EGFR kinase inhibitors and other additional agents can beadministered either separately or together by the same or differentroutes, and in a wide variety of different dosage forms. For example,the EGFR kinase inhibitor is preferably administered orally orparenterally. Where the EGFR kinase inhibitor is erlotinib HCl(TARCEVA™), oral administration is preferable. Both the EGFR kinaseinhibitor and other additional agents can be administered in single ormultiple doses.

The EGFR kinase inhibitor can be administered with variouspharmaceutically acceptable inert carriers in the form of tablets,capsules, lozenges, troches, hard candies, powders, sprays, creams,salves, suppositories, jellies, gels, pastes, lotions, ointments,elixirs, syrups, and the like. Administration of such dosage forms canbe carried out in single or multiple doses. Carriers include soliddiluents or fillers, sterile aqueous media and various non-toxic organicsolvents, etc. Oral pharmaceutical compositions can be suitablysweetened and/or flavored.

The EGFR kinase inhibitor can be combined together with variouspharmaceutically acceptable inert carriers in the form of sprays,creams, salves, suppositories, jellies, gels, pastes, lotions,ointments, and the like. Administration of such dosage forms can becarried out in single or multiple doses. Carriers include solid diluentsor fillers, sterile aqueous media, and various non-toxic organicsolvents, etc.

All formulations comprising proteinaceous EGFR kinase inhibitors shouldbe selected so as to avoid denaturation and/or degradation and loss ofbiological activity of the inhibitor.

Methods of preparing pharmaceutical compositions comprising an EGFRkinase inhibitor are known in the art, and are described, e.g. inInternational Patent Publication No. WO 01/34574. In view of theteaching of the present invention, methods of preparing pharmaceuticalcompositions comprising an EGFR kinase inhibitor will be apparent fromthe above-cited publications and from other known references, such asRemington's Pharmaceutical Sciences, Mack Publishing Company, Easton,Pa., ₁₈th edition (1990).

For oral administration of EGFR kinase inhibitors, tablets containingone or both of the active agents are combined with any of variousexcipients such as, for example, micro-crystalline cellulose, sodiumcitrate, calcium carbonate, dicalcium phosphate and glycine, along withvarious disintegrants such as starch (and preferably corn, potato ortapioca starch), alginic acid and certain complex silicates, togetherwith granulation binders like polyvinyl pyrrolidone, sucrose, gelatinand acacia. Additionally, lubricating agents such as magnesium stearate,sodium lauryl sulfate and talc are often very useful for tabletingpurposes. Solid compositions of a similar type may also be employed asfillers in gelatin capsules; preferred materials in this connection alsoinclude lactose or milk sugar as well as high molecular weightpolyethylene glycols. When aqueous suspensions and/or elixirs aredesired for oral administration, the EGFR kinase inhibitor may becombined with various sweetening or flavoring agents, coloring matter ordyes, and, if so desired, emulsifying and/or suspending agents as well,together with such diluents as water, ethanol, propylene glycol,glycerin and various like combinations thereof.

For parenteral administration of either or both of the active agents,solutions in either sesame or peanut oil or in aqueous propylene glycolmay be employed, as well as sterile aqueous solutions comprising theactive agent or a corresponding water-soluble salt thereof. Such sterileaqueous solutions are preferably suitably buffered, and are alsopreferably rendered isotonic, e.g., with sufficient saline or glucose.These particular aqueous solutions are especially suitable forintravenous, intramuscular, subcutaneous and intraperitoneal injectionpurposes. The oily solutions are suitable for intra-articular,intramuscular and subcutaneous injection purposes. The preparation ofall these solutions under sterile conditions is readily accomplished bystandard pharmaceutical techniques well known to those skilled in theart. Any parenteral formulation selected for administration ofproteinaceous EGFR kinase inhibitors should be selected so as to avoiddenaturation and loss of biological activity of the inhibitor.

Additionally, it is possible to topically administer either or both ofthe active agents, by way of, for example, creams, lotions, jellies,gels, pastes, ointments, salves and the like, in accordance withstandard pharmaceutical practice. For example, a topical formulationcomprising an EGFR kinase inhibitor in about 0. 1% (w/v) to about 5%(w/v) concentration can be prepared.

For veterinary purposes, the active agents can be administeredseparately or together to animals using any of the forms and by any ofthe routes described above. In a preferred embodiment, the EGFR kinaseinhibitor is administered in the form of a capsule, bolus, tablet,liquid drench, by injection or as an implant. As an alternative, theEGFR kinase inhibitor can be administered with the animal feedstuff, andfor this purpose a concentrated feed additive or premix may be preparedfor a normal animal feed. Such formulations are prepared in aconventional manner in accordance with standard veterinary practice.

As used herein, the term “EGFR kinase inhibitor” refers to any EGFRkinase inhibitor that is currently known in the art or that will beidentified in the future, and includes any chemical entity that, uponadministration to a patient, results in inhibition of a biologicalactivity associated with activation of the EGF receptor in the patient,including any of the downstream biological effects otherwise resultingfrom the binding to EGFR of its natural ligand. Such EGFR kinaseinhibitors include any agent that can block EGFR activation or any ofthe downstream biological effects of EGFR activation that are relevantto treating cancer in a patient. Such an inhibitor can act by bindingdirectly to the intracellular domain of the receptor and inhibiting itskinase activity. Alternatively, such an inhibitor can act by occupyingthe ligand binding site or a portion thereof of the EGF receptor,thereby making the receptor inaccessible to its natural ligand so thatits normal biological activity is prevented or reduced. Alternatively,such an inhibitor can act by modulating the dimerization of EGFRpolypeptides, or interaction of EGFR polypeptide with other proteins, orenhance ubiquitination and endocytotic degradation of EGFR. EGFR kinaseinhibitors include but are not limited to low molecular weightinhibitors, antibodies or antibody fragments, antisense constructs,small inhibitory RNAs (i.e. RNA interference by dsRNA; RNAi), andribozymes. In a preferred embodiment, the EGFR kinase inhibitor is asmall organic molecule or an antibody that binds specifically to thehuman EGFR.

EGFR kinase inhibitors that include, for example quinazoline EGFR kinaseinhibitors, pyrido-pyrimidine EGFR kinase inhibitors,pyrimido-pyrimidine EGFR kinase inhibitors, pyrrolo-pyrimidine EGFRkinase inhibitors, pyrazolo-pyrimidine EGFR kinase inhibitors,phenylamino-pyrimidine EGFR kinase inhibitors, oxindole EGFR kinaseinhibitors, indolocarbazole EGFR kinase inhibitors, phthalazine EGFRkinase inhibitors, isoflavone EGFR kinase inhibitors, quinalone EGFRkinase inhibitors, and tyrphostin EGFR kinase inhibitors, such as thosedescribed in the following patent publications, and all pharmaceuticallyacceptable salts and solvates of said EGFR kinase inhibitors:International Patent Publication Nos. WO 96/33980, WO 96/30347, WO97/30034, WO 97/30044, WO 97/38994, WO 97/49688, WO 98/02434, WO97/38983, WO 95/19774, WO 95/19970, WO 97/13771, WO 98/02437, WO98/02438, WO 97/32881, WO 98/33798, WO 97/32880, WO 97/3288, WO97/02266, WO 97/27199, WO 98/07726, WO 97/34895, WO 96/31510, WO98/14449, WO 98/14450, WO 98/14451, WO 95/09847, WO 97/19065, WO98/17662, WO 99/35146, WO 99/35132, WO 99/07701, and WO 92/20642;European Patent Application Nos. EP 520722, EP 566226, EP 787772, EP837063, and EP 682027; U.S. Pat. Nos. 5,747,498, 5,789,427, 5,650,415,and 5,656,643; and German Patent Application No. DE 19629652. Additionalnon-limiting examples of low molecular weight EGFR kinase inhibitorsinclude any of the EGFR kinase inhibitors described in Traxler, P.,1998, Exp. Opin. Ther. Patents 8(12):1599-1625.

Specific preferred examples of low molecular weight EGFR kinaseinhibitors that can be used according to the present invention include[6,7-bis(2-methoxyethoxy)-4-quinazolin-4-yl]-(3-ethynylphenyl) amine(also known as OSI-774, erlotinib, or TARCEVA™ (erlotinib HCl); OSIPharmaceuticals/Genentech/Roche) (U.S. Pat. No. 5,747,498; InternationalPatent Publication No. WO 01/34574, and Moyer, J. D. et al. (1997)Cancer Res. 57:4838-4848); CI-1033 (formerly known as PD183805; Pfizer)(Sherwood et al., 1999, Proc. Am. Assoc. Cancer Res. 40:723); PD-158780(Pfizer); AG-1478 (University of California); CGP-59326 (Novartis);PKI-166 (Novartis); EKB-569 (Wyeth); GW-2016 (also known as GW-572016 orlapatinib ditosylate; GSK); and gefitinib (also known as ZD1839 orIRESSA™; Astrazeneca) (Woodburn et al., 1997, Proc. Am. Assoc. CancerRes. 38:633). A particularly preferred low molecular weight EGFR kinaseinhibitor that can be used according to the present invention is[6,7-bis(2-methoxyethoxy)-4-quinazolin-4-yl]-(3-ethynylphenyl) amine(i.e. erlotinib), its hydrochloride salt (i.e. erlotinib HCl, TARCEVA™),or other salt forms (e.g. erlotinib mesylate).

Antibody-based EGFR kinase inhibitors include any anti-EGFR antibody orantibody fragment that can partially or completely block EGFR activationby its natural ligand. Non-limiting examples of antibody-based EGFRkinase inhibitors include those described in Modjtahedi, H., et al.,1993, Br. J. Cancer 67:247-253; Teramoto, T., et al., 1996, Cancer77:639-645; Goldstein et al., 1995, Clin. Cancer Res. 1:1311-1318;Huang, S. M., et al., 1999, Cancer Res. 15:59(8):1935-40; and Yang, X.,et al., 1999, Cancer Res. 59:1236-1243. Thus, the EGFR kinase inhibitorcan be the monoclonal antibody Mab E7.6.3 (Yang, X. D. et al. (1999)Cancer Res. 59:1236-43), or Mab C225 (ATCC Accession No. HB-8508), or anantibody or antibody fragment having the binding specificity thereof.Suitable monoclonal antibody EGFR kinase inhibitors include, but are notlimited to, IMC-C225 (also known as cetuximab or ERBITUX™; ImcloneSystems), ABX-EGF (Abgenix), EMD 72000 (Merck KgaA, Darmstadt), RH3(York Medical Bioscience Inc.), and MDX-447 (Medarex/Merck KgaA).

Additional antibody-based EGFR kinase inhibitors can be raised accordingto known methods by administering the appropriate antigen or epitope toa host animal selected, e.g., from pigs, cows, horses, rabbits, goats,sheep, and mice, among others. Various adjuvants known in the art can beused to enhance antibody production.

Although antibodies useful in practicing the invention can bepolyclonal, monoclonal antibodies are preferred. Monoclonal antibodiesagainst EGFR can be prepared and isolated using any technique thatprovides for the production of antibody molecules by continuous celllines in culture. Techniques for production and isolation include butare not limited to the hybridoma technique originally described byKohler and Milstein (Nature, 1975, 256: 495-497); the human B-cellhybridoma technique (Kosbor et al., 1983, Immunology Today 4:72; Cote etal., 1983, Proc. Nati. Acad. Sci. USA 80: 2026-2030); and theEBV-hybridoma technique (Cole et al, 1985, Monoclonal Antibodies andCancer Therapy, Alan R. Liss, Inc., pp. 77-96).

Alternatively, techniques described for the production of single chainantibodies (see, e.g., U.S. Pat. No. 4,946,778) can be adapted toproduce anti-EGFR single chain antibodies. Antibody-based EGFR kinaseinhibitors useful in practicing the present invention also includeanti-EGFR antibody fragments including but not limited to F(ab′).sub.2fragments, which can be generated by pepsin digestion of an intactantibody molecule, and Fab fragments, which can be generated by reducingthe disulfide bridges of the F(ab′).sub.2 fragments. Alternatively, Faband/or scFv expression libraries can be constructed (see, e.g., Huse etal., 1989, Science 246: 1275-1281) to allow rapid identification offragments having the desired specificity to EGFR.

Techniques for the production and isolation of monoclonal antibodies andantibody fragments are well-known in the art, and are described inHarlow and Lane, 1988, Antibodies: A Laboratory Manual, Cold SpringHarbor Laboratory, and in J. W. Goding, 1986, Monoclonal Antibodies:Principles and Practice, Academic Press, London. Humanized anti-EGFRantibodies and antibody fragments can also be prepared according toknown techniques such as those described in Vaughn, T. J. et al., 1998,Nature Biotech. 16:535-539 and references cited therein, and suchantibodies or fragments thereof are also useful in practicing thepresent invention.

EGFR kinase inhibitors for use in the present invention canalternatively be based on antisense oligonucleotide constructs.Anti-sense oligonucleotides, including anti-sense RNA molecules andanti-sense DNA molecules, would act to directly block the translation ofEGFR MRNA by binding thereto and thus preventing protein translation orincreasing mRNA degradation, thus decreasing the level of EGFR kinaseprotein, and thus activity, in a cell. For example, antisenseoligonucleotides of at least about 15 bases and complementary to uniqueregions of the mRNA transcript sequence encoding EGFR can besynthesized, e.g., by conventional phosphodiester techniques andadministered by e.g., intravenous injection or infusion. Methods forusing antisense techniques for specifically inhibiting gene expressionof genes whose sequence is known are well known in the art (e.g. seeU.S. Pat. Nos. 6,566,135; 6,566,131; 6,365,354; 6,410,323; 6,107,091;6,046,321; and 5,981,732).

Small inhibitory RNAs (siRNAs) can also function as EGFR kinaseinhibitors for use in the present invention. EGFR gene expression can bereduced by contacting the tumor, subject or cell with a small doublestranded RNA (dsRNA), or a vector or construct causing the production ofa small double stranded RNA, such that expression of EGFR isspecifically inhibited (i.e. RNA interference or RNAi). Methods forselecting an appropriate dsRNA or dsRNA-encoding vector are well knownin the art for genes whose sequence is known (e.g. see Tuschi, T., etal. (1999) Genes Dev. 13(24):3191-3197; Elbashir, S. M. et al. (2001)Nature 411:494-498; Hannon, G. J. (2002) Nature 418:244-251; McManus, M.T. and Sharp, P. A. (2002) Nature Reviews Genetics 3:737-747;Bremmelkamp, T. R. et al. (2002) Science 296:550-553; U.S. Pat. Nos.6,573,099 and 6,506,559; and International Patent Publication Nos. WO01/36646, WO 99/32619, and WO 01/68836).

Ribozymes can also function as EGFR kinase inhibitors for use in thepresent invention. Ribozymes are enzymatic RNA molecules capable ofcatalyzing the specific cleavage of RNA. The mechanism of ribozymeaction involves sequence specific hybridization of the ribozyme moleculeto complementary target RNA, followed by endonucleolytic cleavage.Engineered hairpin or hammerhead motif ribozyme molecules thatspecifically and efficiently catalyze endonucleolytic cleavage of EGFRmRNA sequences are thereby useful within the scope of the presentinvention. Specific ribozyme cleavage sites within any potential RNAtarget are initially identified by scanning the target molecule forribozyme cleavage sites, which typically include the followingsequences, GUA, GUU, and GUC. Once identified, short RNA sequences ofbetween about 15 and 20 ribonucleotides corresponding to the region ofthe target gene containing the cleavage site can be evaluated forpredicted structural features, such as secondary structure, that canrender the oligonucleotide sequence unsuitable. The suitability ofcandidate targets can also be evaluated by testing their accessibilityto hybridization with complementary oligonucleotides, using, e.g.,ribonuclease protection assays.

Both antisense oligonucleotides and ribozymes useful as EGFR kinaseinhibitors can be prepared by known methods. These include techniquesfor chemical synthesis such as, e.g., by solid phase phosphoramaditechemical synthesis. Alternatively, anti-sense RNA molecules can begenerated by in vitro or in vivo transcription of DNA sequences encodingthe RNA molecule. Such DNA sequences can be incorporated into a widevariety of vectors that incorporate suitable RNA polymerase promoterssuch as the T7 or SP6 polymerase promoters. Various modifications to theoligonucleotides of the invention can be introduced as a means ofincreasing intracellular stability and half-life. Possible modificationsinclude but are not limited to the addition of flanking sequences ofribonucleotides or deoxyribonucleotides to the 5′ and/or 3′ ends of themolecule, or the use of phosphorothioate or 2′-O-methyl rather thanphosphodiesterase linkages within the oligonucleotide backbone.

In the context of the methods of treatment of this invention, EGFRkinase inhibitors are used as a composition comprised of apharmaceutically acceptable carrier and a non-toxic therapeuticallyeffective amount of an EGFR kinase inhibitor compound (includingpharmaceutically acceptable salts thereof).

The term “pharmaceutically acceptable salts” refers to salts preparedfrom pharmaceutically acceptable non-toxic bases or acids. When acompound of the present invention is acidic, its corresponding salt canbe conveniently prepared from pharmaceutically acceptable non-toxicbases, including inorganic bases and organic bases. Salts derived fromsuch inorganic bases include aluminum, ammonium, calcium, copper (cupricand cuprous), ferric, ferrous, lithium, magnesium, manganese (manganicand manganous), potassium, sodium, zinc and the like salts. Particularlypreferred are the ammonium, calcium, magnesium, potassium and sodiumsalts. Salts derived from pharmaceutically acceptable organic non-toxicbases include salts of primary, secondary, and tertiary amines, as wellas cyclic amines and substituted amines such as naturally occurring andsynthesized substituted amines. Other pharmaceutically acceptableorganic non-toxic bases from which salts can be formed include ionexchange resins such as, for example, arginine, betaine, caffeine,choline, N′,N′-dibenzylethylenediamine, diethylamine,2-diethylaminoethanol, 2-dimethylaminoethanol, ethanolamine,ethylenediamine, N-ethylmorpholine, N-ethylpiperidine, glucamine,glucosamine, histidine, hydrabamine, isopropylamine, lysine,methylglucamine, morpholine, piperazine, piperidine, polyamine resins,procaine, purines, theobromine, triethylameine, trimethylamine,tripropylamine, tromethamine and the like.

When a compound used in the present invention is basic, itscorresponding salt can be conveniently prepared from pharmaceuticallyacceptable non-toxic acids, including inorganic and organic acids. Suchacids include, for example, acetic, benzenesulfonic, benzoic,camphorsulfonic, citric, ethanesulfonic, fumaric, gluconic, glutamic,hydrobromic, hydrochloric, isethionic, lactic, maleic, malic, mandelic,methanesulfonic, mucic, nitric, pamoic, pantothenic, phosphoric,succinic, sulfuric, tartaric, p-toluenesulfonic acid and the like.Particularly preferred are citric, hydrobromic, hydrochloric, maleic,phosphoric, sulfuric and tartaric acids.

Pharmaceutical compositions used in the present invention comprising anEGFR kinase inhibitor compound (including pharmaceutically acceptablesalts thereof) as active ingredient, can include a pharmaceuticallyacceptable carrier and optionally other therapeutic ingredients oradjuvants. Other therapeutic agents may include those cytotoxic,chemotherapeutic or anti-cancer agents, or agents which enhance theeffects of such agents, as listed above. The compositions includecompositions suitable for oral, rectal, topical, and parenteral(including subcutaneous, intramuscular, and intravenous) administration,although the most suitable route in any given case will depend on theparticular host, and nature and severity of the conditions for which theactive ingredient is being administered. The pharmaceutical compositionsmay be conveniently presented in unit dosage form and prepared by any ofthe methods well known in the art of pharmacy.

In practice, the EGFR kinase inhibitor compounds (includingpharmaceutically acceptable salts thereof) of this invention can becombined as the active ingredient in intimate admixture with apharmaceutical carrier according to conventional pharmaceuticalcompounding techniques. The carrier may take a wide variety of formsdepending on the form of preparation desired for administration, e.g.oral or parenteral (including intravenous). Thus, the pharmaceuticalcompositions of the present invention can be presented as discrete unitssuitable for oral administration such as capsules, cachets or tabletseach containing a predetermined amount of the active ingredient.Further, the compositions can be presented as a powder, as granules, asa solution, as a suspension in an aqueous liquid, as a non-aqueousliquid, as an oil-in-water emulsion, or as a water-in-oil liquidemulsion. In addition to the common dosage forms set out above, an EGFRkinase inhibitor compound (including pharmaceutically acceptable saltsof each component thereof) may also be administered by controlledrelease means and/or delivery devices. The combination compositions maybe prepared by any of the methods of pharmacy. In general, such methodsinclude a step of bringing into association the active ingredients withthe carrier that constitutes one or more necessary ingredients. Ingeneral, the compositions are prepared by uniformly and intimatelyadmixing the active ingredient with liquid carriers or finely dividedsolid carriers or both. The product can then be conveniently shaped intothe desired presentation.

An EGFR kinase inhibitor compound (including pharmaceutically acceptablesalts thereof) used in this invention, can also be included inpharmaceutical compositions in combination with one or more othertherapeutically active compounds. Other therapeutically active compoundsmay include those cytotoxic, chemotherapeutic or anti-cancer agents, oragents which enhance the effects of such agents, as listed above.

Thus in one embodiment of this invention, the pharmaceutical compositioncan comprise an EGFR kinase inhibitor compound in combination with ananticancer agent, wherein said anti-cancer agent is a member selectedfrom the group consisting of alkylating drugs, antimetabolites,microtubule inhibitors, podophyllotoxins, antibiotics, nitrosoureas,hormone therapies, kinase inhibitors, activators of tumor cellapoptosis, and antiangiogenic agents.

The pharmaceutical carrier employed can be, for example, a solid,liquid, or gas. Examples of solid carriers include lactose, terra alba,sucrose, talc, gelatin, agar, pectin, acacia, magnesium stearate, andstearic acid. Examples of liquid carriers are sugar syrup, peanut oil,olive oil, and water. Examples of gaseous carriers include carbondioxide and nitrogen.

In preparing the compositions for oral dosage form, any convenientpharmaceutical media may be employed. For example, water, glycols, oils,alcohols, flavoring agents, preservatives, coloring agents, and the likemay be used to form oral liquid preparations such as suspensions,elixirs and solutions; while carriers such as starches, sugars,microcrystalline cellulose, diluents, granulating agents, lubricants,binders, disintegrating agents, and the like may be used to form oralsolid preparations such as powders, capsules and tablets. Because oftheir ease of administration, tablets and capsules are the preferredoral dosage units whereby solid pharmaceutical carriers are employed.Optionally, tablets may be coated by standard aqueous or nonaqueoustechniques.

A tablet containing the composition used for this invention may beprepared by compression or molding, optionally with one or moreaccessory ingredients or adjuvants. Compressed tablets may be preparedby compressing, in a suitable machine, the active ingredient in afree-flowing form such as powder or granules, optionally mixed with abinder, lubricant, inert diluent, surface active or dispersing agent.Molded tablets may be made by molding in a suitable machine, a mixtureof the powdered compound moistened with an inert liquid diluent. Eachtablet preferably contains from about 0.05 mg to about 5 g of the activeingredient and each cachet or capsule preferably contains from about0.05 mg to about 5 g of the active ingredient.

For example, a formulation intended for the oral administration tohumans may contain from about 0.5 mg to about 5 g of active agent,compounded with an appropriate and convenient amount of carrier materialthat may vary from about 5 to about 95 percent of the total composition.Unit dosage forms will generally contain between from about 1 mg toabout 2 g of the active ingredient, typically 25 mg, 50 mg, 100 mg, 200mg, 300 mg, 400 mg, 500 mg, 600 mg, 800 mg, or 1000 mg.

Pharmaceutical compositions used in the present invention suitable forparenteral administration may be prepared as solutions or suspensions ofthe active compounds in water. A suitable surfactant can be includedsuch as, for example, hydroxypropylcellulose. Dispersions can also beprepared in glycerol, liquid polyethylene glycols, and mixtures thereofin oils. Further, a preservative can be included to prevent thedetrimental growth of microorganisms.

Pharmaceutical compositions used in the present invention suitable forinjectable use include sterile aqueous solutions or dispersions.Furthermore, the compositions can be in the form of sterile powders forthe extemporaneous preparation of such sterile injectable solutions ordispersions. In all cases, the final injectable form must be sterile andmust be effectively fluid for easy syringability. The pharmaceuticalcompositions must be stable under the conditions of manufacture andstorage; thus, preferably should be preserved against the contaminatingaction of microorganisms such as bacteria and fungi. The carrier can bea solvent or dispersion medium containing, for example, water, ethanol,polyol (e.g., glycerol, propylene glycol and liquid polyethyleneglycol), vegetable oils, and suitable mixtures thereof.

Pharmaceutical compositions for the present invention can be in a formsuitable for topical sue such as, for example, an aerosol, cream,ointment, lotion, dusting powder, or the like. Further, the compositionscan be in a form suitable for use in transdermal devices. Theseformulations may be prepared, utilizing an EGFR kinase inhibitorcompound (including pharmaceutically acceptable salts thereof), viaconventional processing methods. As an example, a cream or ointment isprepared by admixing hydrophilic material and water, together with about5 wt % to about 10 wt % of the compound, to produce a cream or ointmenthaving a desired consistency.

Pharmaceutical compositions for this invention can be in a form suitablefor rectal administration wherein the carrier is a solid. It ispreferable that the mixture forms unit dose suppositories. Suitablecarriers include cocoa butter and other materials commonly used in theart. The suppositories may be conveniently formed by first admixing thecomposition with the softened or melted carrier(s) followed by chillingand shaping in molds.

In addition to the aforementioned carrier ingredients, thepharmaceutical formulations described above may include, as appropriate,one or more additional carrier ingredients such as diluents, buffers,flavoring agents, binders, surface-active agents, thickeners,lubricants, preservatives (including anti-oxidants) and the like.Furthermore, other adjuvants can be included to render the formulationisotonic with the blood of the intended recipient. Compositionscontaining an EGFR kinase inhibitor compound (including pharmaceuticallyacceptable salts thereof) may also be prepared in powder or liquidconcentrate form.

Dosage levels for the compounds used for practicing this invention willbe approximately as described herein, or as described in the art forthese compounds. It is understood, however, that the specific dose levelfor any particular patient will depend upon a variety of factorsincluding the age, body weight, general health, sex, diet, time ofadministration, route of administration, rate of excretion, drugcombination and the severity of the particular disease undergoingtherapy.

Many alternative experimental methods known in the art may besuccessfully substituted for those specifically described herein in thepractice of this invention, as for example described in many of theexcellent manuals and textbooks available in the areas of technologyrelevant to this invention (e.g. Using Antibodies, A Laboratory Manual,edited by Harlow, E. and Lane, D., 1999, Cold Spring Harbor LaboratoryPress, (e.g. ISBN 0-87969-544-7); Roe B. A. et. al. 1996, DNA Isolationand Sequencing (Essential Techniques Series), John Wiley & Sons.(e.g.ISBN 0-471-97324-0); Methods in Enzymology: Chimeric Genes andProteins”, 2000, ed. J. Abelson, M. Simon, S. Emr, J. Thomer. AcademicPress; Molecular Cloning: a Laboratory Manual, 2001, 3^(rd) Edition, byJoseph Sambrook and Peter MacCallum, (the former Maniatis Cloningmanual) (e.g. ISBN 0-87969-577-3); Current Protocols in MolecularBiology, Ed. Fred M. Ausubel, et. al. John Wiley & Sons (e.g. ISBN0-471-50338-X); Current Protocols in Protein Science, Ed. John E.Coligan, John Wiley & Sons (e.g. ISBN 0-471-11184-8); and Methods inEnzymology: Guide to protein Purification, 1990, Vol. 182, Ed.Deutscher, M.P., Acedemic Press, Inc. (e.g. ISBN 0-12-213585-7)), or asdescribed in the many university and commercial websites devoted todescribing experimental methods in molecular biology.

This invention will be better understood from the Experimental Detailsthat follow. However, one skilled in the art will readily appreciatethat the specific methods and results discussed are merely illustrativeof the invention as described more fully in the claims which followthereafter, and are not to be considered in any way limited thereto.

Experimental Details:

Introduction

Inhibitors of EGF receptor function have shown clinical utility and thedefinition of key EGF receptor signaling pathways which describe patientsubsets most likely to benefit from therapy has become an important areaof investigation. Mutations which activate the receptor's intrinsicprotein tyrosine kinase activity and/or increase downstream signalinghave been observed in NSCLC and glioblastoma. However the role ofmutations as a principle mechanism in conferring sensitivity to EGFreceptor inhibitors has been controversial. In vitro and clinicalstudies have shown considerable variability between wt EGF receptor celllines and tumors in their cellular responses to EGF receptor inhibition,which in part has been shown to derive from EGF receptor independentactivation of the phosphatidyl inositol 3-kinase pathway, leading to thecontinued phosphorylation of the anti-apoptotic serine-threonine kinaseAkt. The molecular determinants to alternative routes of PI3-kinaseactivation and consequent EGF receptor inhibitor insensitivity are anactive area of investigation. For example the insulin-like growthfactor-1 receptor (IGF-1 receptor), which strongly activates thePI3-kinase pathway, has been implicated in cellular resistance to EGFinhibitors. The roles of cell-cell and cell-adhesion networks, which canalso exert survival signals through the PI3-kinase pathway in mediatinginsensitivity to selective EGF receptor inhibition are less clear andwould be postulated to impact cell sensitivity to EGF receptor blockade.The ability of tumor cells to maintain growth and survival signals inthe absence of adhesion to extracellular matrix or cell-cell contacts isimportant not only in the context of cell migration and metastasis butalso in maintaining cell proliferation and survival in wound-like tumorenvironments where extracellular matrix is being remodeled and cellcontact inhibition is diminished. Here we demonstrate that sensitivityof NSCLC and pancreatic cells to EGF receptor inhibition is conferred byan E-cadherin epithelial cell phenotype in which ErbB family membersignaling was active. Conversely insensitivity to EGF receptorinhibition was mediated through an epithelial-mesenchymal transition(EMT) associated with the expression of vimentin and/or fibronectin.

Materials and Methods

Cell Culture and Preparation of Cell Extracts

The NSCLC lines with wt EGFR, H292, H358, H322, H441, A549, Calu6, H460,H1703 and SW1573 were cultured in the appropriate ATCC recommendedsupplemented media. Cell extracts were prepared by detergent lysis ((50mM Tris-HCl, pH8, 150 mM NaCl, 1% NP-40, 0.5% NaDeoxycholate, 0.1% SDS)containing protease and phosphatase inhibitors. The soluble proteinconcentration was determined by micro-BSA assay (Pierce, Rockford IL).

Protein Identification and Quantitation by LC-MS/MS Peptide Sequencing

Anti-phosphotyrosine immunoaffinity resins were prepared by covalentcoupling to a solid support by standard methods. Freshly preparedimmunoaffinity resins were used for each biological experiment tomaximize binding and reduce carryover. Briefly, anti-phosphotyrosineantibodies were crosslinked to solid-support and non-covalently boundIgG removed by low pH elution. Fresh affinity resins were prepared foreach biological experiment to avoid cross-contamination. Proteinsisolated by anti-phosphotyrosine affinity selection were measured byiTRAQ labeling of tryptic peptides as previously described (Ross et al,2004; Haley et al., 2004). Peptide masses and sequence information weredetermined by electrospray LC-MS/MS and database searching. Peptideswith confidence levels of >=90% with scores of >=20 were considered,after which spectra were inspected manually. Peptide expression ratioswere converted to log₂ values and averaged to yield a single proteinexpression value for each time point (1, 4 and 24 hours) after erlotinibexposure (1 uM). Proteins were clustered by temporal log₂ proteinexpression ratios using Euclidian hierarchical methods andself-organizing maps.

Immunoblot Analysis of NSCLC and Pancreatic Cell Line Extracts

Protein immunodetection was performed by electrophoretic transfer ofSDS-PAGE separated proteins to nitrocellulose, incubation with antibodyand chemiluminescent second step detection (PicoWest; Pierce, Rockford,Ill). The antibodies included: E-Cadherin (Santa Cruz Biotechnology,Santa Cruz, Calif.; sc21791), α-catenin (sc9988), β-catenin (sc7963),γ-catenin (sc8415) and Brk (sc1188); Vimentin (BD Biosciences, San Jose,Calif.; BD550513) and Fibronectin (BD610077); GAPDH (AbCam, Cambridge,UK); Phospho-Akt (Cell Signaling, Beverly, Mass. #9271), Akt (CS,#9272), Phospho-p44/42 Map kinase^(T202/Y204) (Erk1/2;CS #9101),Phospho-Src family^(Y416) (CS #2101), Phospho-STAT3^(Y705) (CS, #9131)and Phospho-S6^(S235/236) (CS, #2211); β-actin (Sigma, Saint Louis, Mo.#A5441). Antibodies further included: Phospho-Shc (Cell Signaling,#2434, Beverly, Mass.), Phospho-Paxillin (Cell Signaling, #2541),Phospho-Akt (Ser473 and Thr308) (Cell Signaling, #9271 and 9275),Phospho-HER2/ErbB2 (Cell Signaling, #2245), Phospho-Her3 (Tyr1289) (CellSignaling #4791), Phospho-p44/42 Map kinase (Cell Signaling, #9101),Phospho-EGFR (Tyr845) (Cell Signaling, #2231), Phospho-EGFR (Tyr992)(Cell Signaling, #2235), Phospho-EGFR (Tyr1045) (Cell Signaling, #2237),EGFR (Cell Signaling, #2232), Phospho-p70 S6 kinase (Cell Signaling,#9205), Phospho-GSK-3alpha/beta (Cell Signaling, #9331), Phospho-EGFR(Tyr1068) (Cell Signaling, #2236), Phospho-Src family (Tyr416) (CellSignaling #2101), phospho-SAPK/JNK (Thr183/Tyr185)(Cell Signaling#9251), phospho-STAT3 (Tyr705) (Cell Signaling #9131), ErbB2 (CellSignaling #2242); ErbB4 (Cell Signaling 4795), PY20 (Exalpha BiologicalsInc.), Brk (Santa Cruz Biochemicals).

In vitro Pharmacology

On day 1, NSCLC cells were plated 3-5×10⁴ cells/well in 96 well platesin their normal serum-containing media. After 24 h, erlotinib was addedto the plates at a 10× concentration in a 10% DMSO/water solution toachieve a final assay concentration range from 20 μM to 8 nM. Dilutionswere made in 3-fold steps. Final DMSO concentrations in each well wasconstant and did not exceed 1%. Following erlotinib addition, cells werereplaced in the incubator and left for 72 h. On day 5, Cell-Titer Glo(Promega) was used to assess the effects on cell viability.Manufacturers instructions were followed for the assay. Experiments wereconducted in triplicate to at least an n=3. Data was normalized as apercentage inhibition compared to DMSO only control wells andconcentration-response analysis was performed using Prizm graphingsoftware.

In vivo Pharmacology

Female CD-1 nu/nu mice (Charles River Laboratories) were implanted withharvested NSCLC tumor cells in a single subcutaneous site on the flankof the mice in the axillary region. Tumors were allowed to grow to200±50 mm³, at which time the animals were sorted into treatment groupsof 8 animals per group based on weight (±1 g body weight) and tattooedon the tail for permanent identification. Tumor volumes and body weightswere determined twice weekly. The tumor volume was determined bymeasuring in two directions with vernier calipers and calculated usingthe formula: Tumor volume =(length×width²)/2. The data were plotted asthe % change in mean values of tumor volume and body weight for eachgroup. The tumor growth inhibition (% TGI) was determined as %TGI=100(1−W_(t)−W_(c)): where W_(t) is the median tumor volume of thetreated group at time x and W_(c) is the median tumor volume of thecontrol group at time x. TARCEVA™ was dosed in a 6% Captisol (CyDex,Inc) in WFI (Water for Injection) solution and all control animals weredosed with an equal volume of the vehicle. Tumor growth inhibitionstudies were dosed by oral gavage once a day for 14 days.Pharmacodynamic studies were dosed by oral gavage for 1-3 days withtumors from 4 control and 4 TARCEVA™ treated animals harvested and snapfrozen in liquid nitrogen 4 hours after dosing on Days 1, 2 and 3.

Confocal Microscopy

Cells grown on glass coverslips for 24 hours were washed and fixed with3.7% formaldehyde in PBS followed by permeabilization in 0.5% NP-40. Thecells were washed, blocked with 5% BSA and incubated with primaryantibody for 2 hours at room temperature and with dilutedFITC-conjugated secondary antibody for 1 hour. Nuclei were stained withDAPI (300 nM for 5 min). The confocal images were captured using aspinning objective confocal microscope at 60× magnification.

Results TABLE 2 Growth inhibition of wt EGF receptor tumor cell linessensitive or relatively insensitive to erlotinib expressed asconcentration (μM) required for half-maximal efficacy (EC₅₀) and maximuminhibition (%) by erlotinib. Tumor growth inhibition (TGI) is given forday 15 after xenograft exposure to erlotinib. Max. % TGI EC₅₀ Half Cellline Inhibition (%) Day 15 Maximal Classification H292 69 85 0.1Sensitive H322 80 nd 0.4 Sensitive H358 72 25 0.6 Sensitive H441 55 60 2Sensitive A549 30 49 5 Intermediate H460 30 6 5 Insensitive Calu6 460 >10 Insensitive H1703 30 nd 7 Insensitive SW1573 25 nd 9 Insensitive

NSCLC Lines Containing wt EGF Receptor Display a Range of Sensitivitiesto Erlotinib in vitro

NSCLC cell lines containing mutations in the catalytic domain of EGFRdisplayed hypersensitivity to treatment with the selective EGFRinhibitors erlotinib and gefitinib. It has been suggested that onlythose patients bearing such mutations would respond and/or show survivalbenefit from treatment with EGFR tyrosine kinase inhibitors. However, arandomized placebo controlled clinical trial conducted with erlotinibindicated that the survival rate of patients exposed to the drug waswell in excess of the predicted occurrence of such mutations in thepatient population. This suggested that, although mutations were anindicator of patient response, other factors were undoubtedly involvedin conferring survival benefit.

Initially the receptor for epidermal growth factor (EGFR) was sequencedin 14 NSCLC cell lines. Sequence analysis demonstrated that the EGFRexpressed in all of the cell lines of this study was wild-type withrespect to two recently identified mutations (deletion and pointmutations; data not shown). Having determined that the receptors werewild-type, the sensitivity of the panel of non- small cell lung cancercell lines to erlotinib was assessed using a cell viability assay.

Analysis of erlotinib sensitivity in a range of human NSCLC cell lines,which are wild type for EGFR, indicated a wide range of sensitivity(Table 2; Griffin et al., 2005). We have thus broadly classified thesecell lines into those that are relatively insensitive (H1703, SW1573,H460 and Calu6), those which show an intermediate sensitivity (A549) andthose which are sensitive (H441, H358, H322 and H292) toerlotinib-mediated growth inhibition in vitro and in xenografts. Thesedifferences can be correlated in part to a failure of the relativelyinsensitive cell lines to show erlotinib-mediated inhibition of Akt/PKBphosphorylation (Griffin et al., 2005). A range of sensitivities of thecells to erlotinib was observed from cells lines ranging from the mostsensitive (H292) through the least sensitive (H460). There were fewcorrelations between tumor type and erlotinib sensitivity, although itis interesting to note that both of the bronchioalveolar carcinoma (BAC)derived cell lines (H358 and H322) showed a level of sensitivity to EGFRinhibition. Previous reports from clinical trials have suggested that ofthe population of NSCLC patients, those with BAC histologies tended tohave a greater treatment benefit than other NSCLC patients. However,more BAC derived cell lines should be tested prior to making anyconclusions. The data from the in vitro pharmacology experiments issummarized in Table 2. The concentration response curves were analyzedin two ways. Firstly in order to define the more traditionally acceptedIC50 values (not shown), the curves have been fit in a 0-100% range.However, since erlotinib and other EGFR inhibitors may be described ascytostatic rather than cytotoxic, and therefore would therefore never beexpected to achieve complete cell kill, it is questionable how relevantan IC50 value is. Indeed, even in the most sensitive lines a maximalefficacy of about 70-80% was the most observed. Therefore, an EC50constraining the curves from 0-80% is a more relevant potencycomparison.

In order to determine the relevance of the in vitro cell viability assayto in vivo efficacy, a selection of cell lines ranging from sensitivethrough insensitive in vitro were tested in mouse xenograft models. Thedata from these experiments are shown in FIG. 1 and Table 2. Thecorrelation between in vitro sensitivity and in vivo sensitivity toerlotinib was striking. Those cells that were most sensitive in vitro,were also the most sensitive in vivo, with the rank order ofsensitivities of all cell lines being identical between the two assays.Such a finding strongly supports the use of the in vitro assay as aninitial guide for assessing erlotinib sensitivity in xenograft models.The cell lines chosen were picked for their range of sensitivities basedon in vitro and in vivo activities. Although a somewhat subjectiveclassification, two sensitive lines (H292 and H358), two intermediate(H441 and A549) and two insensitive (H460 and Calu-6) were selected.Despite its low sensitivity in vitro, A549 were classed as anintermediate cell line due to a low level of response in vivo. Theprinciple aim of further study was to determine the moleculardeterminants of erlotinib sensitivity in these NSCLC cell lines.

Changes in Epithelial and Mesenchymal Cell Markers Correlate withSensitivity of NSCLC Cell Lines to Erlotinib

Initially differences in protein tyrosine phosphorylation and complexformation between NSCLC lines sensitive or relatively insensitive toerlotinib in vitro and in xenograft models were measured. Theseexperiments involved anti-phosphotyrosine affinity selection of celllysates, tryptic digestion and protein identification based on LC-MS/MSfragment ion spectra. We observed a striking difference between theerlotinib sensitive and relatively insensitive NSCLC lines in theabnormal expression vimentin and or fibronectin (FIG. 2A). Typicallyvimentin and fibronectin expression are characteristic of mesenchymalcells and are only weakly or unexpressed in epithelial cell lineages.Vimentin expression was primarily found in H1703 and Calu6, whilefibronectin expression was observed in H460 cells. These three NSCLClines were relatively insensitive to growth inhibition by erlotinib invitro (>10 uM EC₅₀) and in vivo (at 200 mg/kg orally qd). Little or novimentin or fibronectin expression was found in the erlotinib sensitiveNSCLC lines H292 and H358, the intermediate line A549 or in the twomutant EGF receptor cell lines H1650 and H1975.

Based on the expression of mesenchymal proteins in NSCLC linesrelatively insensitive to erlotinib, we analyzed protein extracts fromthe same panel of relatively insensitive and sensitive NSCLC cell linesfor the presence or absence of markers characteristic of eitherepithelial or mesenchymal phenotypes (FIG. 2B). Strikingly, E-cadherinwas detected in the sensitive cell lines (H441, H358, H322 and H292) butwas absent in the relatively insensitive cell lines (H1703, SW1573, H460and Calu6). The intermediately sensitive cell line A549 showed low butdetectable expression. A similar loss of γ-catenin was observed in cellsrelatively insensitive to erlotinib, with the exception of H460.Therefore, the relatively insensitive cell lines appear to have lostexpression of epithelial cell marker proteins. Next we asked whetherthese cell lines expressed the mesenchymal markers fibronectin and/orvimentin. The relatively insensitive cell lines clearly expressed eitherone or both of fibronectin and vimentin (FIG. 2B), whereas neitherprotein was detectable in cell lines sensitive to erlotinib.Interestingly the intermediately sensitive cell line A549 again showedlow but detectable levels of both proteins. However, confocal microcopyexperiments (results not shown) using immunostaining with antibodiesspecific for E-cadherin and vimentin indicated that the A549 cellculture used appears to be a mixed population of cells since no dualstaining of cells was observed. This could also explain the somewhatvariable results obtained with this cell line, and is consistent withits intermediate sensitivity to erlotinib.

The changes in cell-lineage markers were further analyzed in tworelatively insensitive and two sensitive cell lines by confocalmicroscopy after immunostaining with antibodies toward E-cadherin andvimentin (FIG. 2C). No E-cadherin staining could be detected in eitherH1703 or Calu6 cells (FIG. 2C, panels 1 and 2), whereas all of thesecells could be stained for vimentin (FIG. 2C, panels 5 and 6). Thereverse was true for the sensitive cell lines H441 and H292, with clearE-cadherin staining on the membrane of these cells (FIG. 2C, panels 3and 4) but no visible vimentin staining (FIG. 2C, panels 7 and 8). Takentogether these data indicate that NSCLC cells which were relativelyinsensitive to growth inhibition by erlotinib appeared to have undergonetransition to a more mesenchymal cell type and expressed either vimentinor fibronectin. In contrast cell lines that were sensitive to growthinhibition by erlotinib maintained an epithelial phenotype and expressedE-cadherin.

Erlotinib Sensitivity Correlates with Maintenance of Epithelial MarkersDuring Tumor Growth in vivo

Tumors xenografts derived from NSCLC cell lines grown in mice displayeda similar degree of erlotinib sensitivity to that observed for therespective cell line in vitro. We therefore wished to examine whetherthe protein markers identified in vitro were also predictive oferlotinib sensitivity in vivo. Protein extracts were prepared from 3independent tumor xenografts grown from H460, Calu6, A549, H441 and H292cells. Immunoblotting of extracts indicated that E-cadherin was notdetectably expressed in the xenografts derived from the H460 and Calu6cells that are relatively insensitive to erlotinib, was expressed at lowlevels in xenografts derived from the A549 cells of intermediatesensitivity and expressed at high levels in H441 and H292 cell linessensitive to erlotinib (FIG. 3). A similar result was observed onanalysis of γ-catenin levels. In contrast xenograft samples derived fromCalu6 expressed fibronectin and vimentin (Calu6) or fibronectin alone(H460), a result consistent with that obtained from in vitro cellcultures (FIG. 2B). H441 and H292 derived xenograft extracts showedlittle or no expression of either fibronectin or vimentin. These in vivoresults further support the in vitro data and indicate that the presenceof these protein markers is not an artifact of cell culture. Further,they support the hypothesis that erlotinib sensitivity may be restrictedto cells with an epithelial phoenotype and that cells which haveundergone EMT become less dependent upon EGFR signaling for cellproliferation and survival.

Expression of Brk in NSCLC Cell Lines that are Relatively Insensitive orSensitive to EGF Receptor Inhibition

The results of these experiments led to the working hypothesis thaterlotinib sensitivity is determined by the ability of the compound toinhibit Akt signaling. Following this hypothesis the question arises asto what is unique about these cells that allows the EGFR pathway to sosignificantly impact cellular Akt signaling. Recent papers by (REFS)have suggested an interesting potential link between EGFR and Aktsignaling, which may or may not involve heterodimerization with otherHer members such as ErbB3, involving the non receptor tyrosine kinaseBrk (also known as PTK6). It was of interest therefore to determinewhether there may be any relationship between Brk expression insensitive and insensitive erlotinib lines, thus providing a rationalefor why EGFR inhibition is so intricately linked to Akt in sensitivecompared to insensitive. FIG. 4 shows Western blot analysis of a numberof lines from the NSCLC panel, and their respective expression of Brkprotein. Interestingly there is a very good correlation between Brklevels and erlotinib sensitivity in so far as high Brk expressionequates to higher erlotinib sensitivity and absence, or lowerexpression, of Brk tends to characterize insensitive lines.

Analysis of EMT Markers is Predictive of Erlotinib Sensitivity ofPancreatic Cell Lines in Culture

We next extended these studies to ask whether these observations wouldbe applicable to other cancer cell types. As erlotinib has shownefficacy in Phase III combination studies with gemcitabine in pancreaticcancer, we examined the sensitivity of pancreatic cell lines to growthinhibition by erlotinib in vitro and their expression of epithelial andmesenchymal lineage markers. Consistent with data in NSCLC, pancreaticcell lines sensitive to erlotinib expressed E-cadherin but not vimentinor fibronectin, while pancreatic lines that are relatively insensitiveto erlotinib had lost E-cadherin expression and gained vimentin and/orfibronectin expression (FIG. 5). These results were observed both byimmunoblot (FIG. 5A) and confocal fluorescence microscopy studies (FIG.5B).

Patients with Tumors Expressing High Levels of E-cadherin have GreaterTime to Disease Progression when Treated with Erlotinib+ChemotherapyCompared to Chemotherapy Treatment Alone

Samples from patients who participated in a randomized, double-blindedphase III clinical trial referred to as Tribute were analyzed forE-cadherin expression by Immunohistochemistry (IHC). Tribute studied1,079 patients at approximately 150 centers in the United States havinghistological confirmed NSCLC who had not received prior chemotherapycomparing erlotinib+chemotherapy (carboplatin/paclitaxel) withchemotherapy alone. Patients received paclitaxel (200 mg/m² 3 hour i.v.infusion) followed by carboplatin (AUC=6 mg/ml×minute infused over 15-30minutes using Calvert formula) with or without erlotinib (100 mg/dayp.o. escalated to 150 mg/day for tolerant patients). Tumor samples,formalin-fixed paraffin-embedded blocks or unstained slides, from 87patients in the Tribute trial were immunostained to detect E-cadherinexpression. Staining intensity was scored as 0, 1+, 2+ and 3+ with 65 ofthe 87 samples having >=2 staining intensity and 22 had <=1 stainingintensity.

Immunohistochemistry for E-cadherin was performed on formalin-fixedparaffin embedded tissue sections assembled in a tissue microarray.Following deparaffinization, antigen retrieval was performed bypretreating with Target Retrieval Solution at 110 degrees C. for 20 min(DakoCytomation, Carpenteria Calif.). The pretreated sections were thenincubated with primary mouse monoclonal IgG2 antibody against E-cadherin(clone 36, Pharmingen) at a concentration of 1 microgram/ml for 60 minat ambient temperature. Primary antibody bound to the sections wasdetected using biotinylated horse anti-mouse IgG, and visualized usingthe avidin-biotin peroxidase complex technique (Vectastain ABC Elite,Vector Laboratories) and diaminobenzidine as chromagen.

It was determined that patients whose tumors stained for high levels ofmembrane and cytoplasmic E-cadherin exhibited significantly longer timeto disease progression (TTP) when treated with the combination oferlotinib and chemotherapy compared to chemotherapy alone (34.0 weeks v.19.3 weeks, p=0.0028). The results are provided in table 2 and areillustrated by the Kaplan-Meier curve in FIG. 6 a. Conversely, patientswhose tumors had low membrane and cytoplasmic E-cadherin expression(staining intensity of <=1) did not have a significant difference in TTPfor the two treatment groups which is illustrated by the Kaplan-Meiercurve in FIG. 6 b. TABLE 2 Time to Progression by E-cadherin stainingfor erlotinib + chemotherapy and chemotherapy alone treatment groupsIntensity >=2 Intensity <=1 Erlotinib + Erlotinib + Chemo chemo Chemochemo N 37 28 14  8 Patients who 31 (83.8%) 16 (57.1%) 8 (57.1%) 5(62.5%) progressed Censored patients  6 (16.2%) 12 (42.9%) 6 (42.9%) 3(37.5%) Median time (wk) 19.3 34.0 30.0 19.1 95% CI (12.9, 25.7) (13.1,42.1) (19.1, .) (8.6, .) P-Value  0.0028  0.3976 (Logrank) Hazard ratio(HR)  0.37  1.63 95% CI for HR (0.19, 0.73) (0.50, 5.33)

Conclusion

The loss of E-cadherin expression and the acquisition of a moremesenchymal phenotype has been shown to correlate with poor prognosis inmultiple epithelial-derived solid tumors. The loss of E-cadherin and toa lesser extent γ-catenin and Brk correlated with cellular and xenograftinsensitivity to EGF receptor inhibition. Conversely the cellularacquisition of mesenchymal markers, vimentin, fibronectin or fibrillincorrelates with a loss of sensitivity to EGF receptor inhibitors. Weclearly show that a partial or complete epithelial to mesenchymaltransition negatively impacts cellular responses to EGF receptorinhibitors in vitro and in xenografts and serves a diagnostic forpatients most likely to benefit from EGF receptor kinase inhibitors andanti-EGF receptor antibody therapies.

Abbreviations

EGF, epidermal growth factor; EMT, epithelial to mesenchymal transition;NSCLC, non-small cell lung carcinoma; HNSCC, head and neck squamous cellcarcinoma; CRC, colorectal cancer; MBC, metastatic breast cancer; EGFR,epidermal growth factor receptor; Brk, Breast tumor kinase (also knownas protein tyrosine kinase 6 (PTK6)); LC, liquid chromatography; MS,mass spectrometry; IGF-1, insulin-like growth factor-1; TGFα,transforming growth factor alpha; HB-EGF, heparin-binding epidermalgrowth factor; LPA, lysophosphatidic acid; TGFα, transforming growthfactor alpha; IC₅₀, half maximal inhibitory concentration; pY,phosphotyrosine; wt, wild-type; PI3K, phosphatidyl inositol-3 kinase;GAPDH, Glyceraldehyde 3-phosphate dehydrogenase.

Incorporation by Reference

All patents, published patent applications and other referencesdisclosed herein are hereby expressly incorporated herein by reference.

Equivalents

Those skilled in the art will recognize, or be able to ascertain, usingno more than routine experimentation, many equivalents to specificembodiments of the invention described specifically herein. Suchequivalents are intended to be encompassed in the scope of the followingclaims.

1. A method of predicting whether a cancer patient is afflicted with atumor that will respond effectively to treatment with an EGFR kinaseinhibitor, comprising: assessing the level of an epithelial biomarkerexpressed by cells of the tumor; and predicting if the tumor willrespond effectively to treatment with an EGFR kinase inhibitor, whereinhigh expression levels of tumor cell epithelial biomarkers correlatewith a tumor that will respond effectively to treatment with an EGFRkinase inhibitor, wherein the epithelial biomarker is selected from Brk,γ-catenin, α1-catenin, α2-catenin, α3-catenin, keratin 8, keratin 18,connexin 31, plakophilin 3, stratafin 1, laminin alpha-5 and ST14. 2.The method of claim 1, wherein the EGFR kinase inhibitor compriseserlotinib.
 3. A method of predicting whether a cancer patient isafflicted with a tumor that will respond effectively to treatment withan EGFR kinase inhibitor, comprising: assessing the level of amesenchymal biomarker expressed by cells of the tumor; and predicting ifthe tumor will respond effectively to treatment with an EGFR kinaseinhibitor, wherein high expression levels of tumor cell mesenchymalbiomarkers correlate with a tumor that will respond less effectively totreatment with an EGFR kinase inhibitor, wherein the mesenchymalbiomarker is selected from vimentin, fibronectin, fibrillin-1,fibrillin-2, collagen alpha-2(IV), collagen alpha-2(V), LOXL1, nidogen,C11 orf9, tenascin, embryonal EDB⁺ fibronectin, tubulin alpha-3 andepimorphin.
 4. The method of claim 3, wherein the EGFR kinase inhibitorcomprises erlotinib.
 5. A method of predicting the sensitivity of tumorcell growth to inhibition by an EGFR kinase inhibitor, comprising:assessing the level of one or more epithelial biomarkers expressed by atumor cell; and predicting the sensitivity of tumor cell growth toinhibition by an EGFR kinase inhibitor, wherein simultaneous highexpression levels of all of the tumor cell epithelial biomarkerscorrelates with high sensitivity to inhibition by EGFR kinaseinhibitors.
 6. The method of claim 5, wherein the one or more epithelialbiomarkers comprises E-cadherin and Brk.
 7. The method of claim 5,wherein the one or more epithelial biomarkers comprises E-cadherin andγ-catenin.
 8. The method of claim 5, wherein the EGFR kinase inhibitorcomprises erlotinib.
 9. A method of predicting the sensitivity of tumorcell growth to inhibition by an EGFR kinase inhibitor, comprising:assessing the level of one or more mesenchymal biomarkers expressed by atumor cell; and predicting the sensitivity of tumor cell growth toinhibition by an EGFR kinase inhibitor, wherein simultaneous low orundetectable expression levels of all of the tumor cell mesenchymalbiomarkers correlates with high sensitivity to inhibition by EGFR kinaseinhibitors.
 10. The method of claim 9, wherein the one or moremesenchymal biomarkers comprises vimentin and fibronectin
 11. The methodof claim 9, wherein the EGFR kinase inhibitor comprises erlotinib.
 12. Amethod of predicting the sensitivity of tumor cell growth to inhibitionby an EGFR kinase inhibitor, comprising: assessing the level of anepithelial biomarker expressed by a tumor cell; assessing the level of amesenchymal biomarker expressed by a tumor cell; and predicting thesensitivity of tumor cell growth to inhibition by an EGFR kinaseinhibitor, wherein a high ratio of epithelial to mesenchymal biomarkerexpression levels correlates with high sensitivity to inhibition by EGFRkinase inhibitors.
 13. The method of claim 12, wherein the epithelialbiomarker comprises E-cadherin and the mesenchymal biomarker comprisesfibronectin.
 14. The method of claim 12, wherein the epithelialbiomarker comprises Brk and the mesenchymal biomarker comprisesfibronectin.
 15. The method of claim 12, wherein the epithelialbiomarker comprises E-cadherin and the mesenchymal biomarker comprisesvimentin.
 16. The method of claim 12, wherein the epithelial biomarkercomprises γ-catenin and the mesenchymal biomarker comprises fibronectin.17. The method of claim 12, wherein the EGFR kinase inhibitor compriseserlotinib.
 18. A method for treating tumors or tumor metastases in apatient, comprising the steps of: diagnosing a patient's likelyresponsiveness to an EGFR kinase inhibitor by assessing whether thetumor cells have undergone an epithelial-mesenchymal transition: andadministering to said patient a therapeutically effective amount of anEGFR kinase inhibitor.
 19. The method of claim 18, wherein the EGFRkinase inhibitor comprises erlotinib.
 20. The method of claim 18,wherein one or more additional anti-cancer agents are co-administeredsimultaneously or sequentially with the EGFR kinase inhibitor.
 21. Amethod for the identification of an agent that enhances sensitivity ofthe growth of a tumor cell to an EGFR kinase inhibitor, said tumor cellhaving being characterized as one that has previously undergone anepithelial-mesenchymal transition, comprising contacting a sample ofsaid tumor cells with an EGFR kinase inhibitor, contacting an identicalsample of said tumor cells with an EGFR kinase inhibitor in the presenceof a test agent, comparing the EGFR kinase inhibitor-mediated growthinhibition in the presence and absence of the test agent, anddetermining whether the test agent is an agent that enhances sensitivityof the growth of the tumor cell to an EGFR kinase inhibitor.